The advent of mass spectrometry based analytical technologies coupled with multivariate statistical methods offers tremendous new opportunities for understanding the pharmacokinetics of multicomponent herbal medicines. In recent years, Jia’s group proposed a polyPK strategy, in a few review papers (Science 2015, Current Drug Metabolism 2010, Evidence-Based Complementary and Alternative Medicine 2013), to characterize the concentration-time profile and the metabolic response profile of multicomponent drugs, using an integrated phytochemical and metabolomics approach. The brand new strategy has been successfully applied in examining the complex pharmacokinetics and pharmacodynamics profiles of tea (Journal of Proteome Research 2012) and Huangqi decoction (Clinical Pharmacology & Therapeutics 2016). This package is the first implementation of the polyPK strategy with 10 easy-to-use functions. The absorbed drug constitutes, the downstream metabolites of the drug constituents and the endogenous metabolites impacted by them can be identified. The association of different types of compounds and their alterations along time can be illustrated by various figures and tables. The representative PK parameters of all compounds can be calculated.
10 functions of the package of polyPK: DataPre,GetDiffData,GetEndo,GetAbso,GetSecdAbso,PKs,Simi,ScatPlot,HeatMap,CorrPlot
DataPrePreprocess the input data. Variables with a lot of zeros and outliers may be removed. Missing values may be imputed and filled by various methods. Data may be transformed by logarithm transformation.
library(polyPK)data("postData")
pred_post<-polyPK::DataPre(tes=postData,mv="min",rz=80,sv=TRUE,log=FALSE,filepath=getwd())An example of preprocessed post-dose dataset:
pred_post[c(1:10),c(1:10)]## Name ID m.z RT.min. X1.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 1
## 3 timepoints(h) <NA> <NA> 0.083
## 4 octanoyl-rac-glycerol inx0001 219.1401 3.5638000 3.72e+03
## 5 1,2,3-propanetricarboxylic acid HMDB31193 73.0000 15.6571820 1.25e+07
## 6 tryptophan HMDB00929 203.0819 1.3524000 7.24e+04
## 7 n-octadecanoic acid HMDB00827 283.2634 9.9524000 4.40e+06
## 8 myristic acid HMDB00806 227.2009 6.8607667 3.78e+05
## 9 glycolithocholic acid HMDB00698 432.3107 3.4209000 3.10e+01
## 10 3-indolelactic acid HMDB00671 203.0000 21.2330824 3.73e+04
## X1.2 X1.3 X1.4 X1.5 X1.6
## 1 1 1 1 1 2
## 2 1 1 1 1 1
## 3 0.083 0.083 0.083 0.083 0.083
## 4 1.62e+03 2.91e+03 4.73e+03 3.78e+03 1.90e+03
## 5 1.63e+07 9.99e+06 1.54e+07 1.82e+07 1.27e+07
## 6 9.80e+04 1.14e+05 9.10e+04 9.62e+04 6.97e+04
## 7 4.36e+06 4.23e+06 2.24e+06 2.42e+06 2.65e+06
## 8 7.13e+05 7.07e+05 3.12e+05 4.87e+05 4.55e+05
## 9 4.79e+00 2.82e+02 2.82e+02 2.82e+02 2.82e+02
## 10 8.52e+04 4.87e+04 4.87e+04 3.79e+04 4.87e+04SimiA function which can get the similar metabolites of two datas.Especially the similar metabolites between drug and pre-dose metabolites.
data("preData")
data("drugData")
Simi(data1<-preData,data2<-drugData,filepath=getwd())## $`repetitive rates in data1`
## [1] 0.3076923
##
## $`repetitive rates in data2`
## [1] 0.6666667
##
## $`similar metabolites`
## data1[-c(1:3), 2]
## [1,] "HMDB00205"
## [2,] "HMDB00806"
## [3,] "HMDB00827"
## [4,] "inx0001"GetDiffDataA function to get all the differential compounds between the pre-dose and every post-dose datasets:
data("preData")
data("postData")
data("design")
data("simidata")
dif<-GetDiffData(preData,postData,simidata,mv="min",rz=80,sv=TRUE,log=FALSE,t="Ttest",r.adj="fdr",filepath=getwd(),design=FALSE)
#'An example of the differential compounds, with preprocessed data:
prepoA<-dif$A
as.data.frame(prepoA)## Name ID m.z RT.min. X0.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 0
## 3 timepoints(h) <NA> <NA> 0
## 110 octanoyl-rac-glycerol inx0001 219.1401 3.563800 4180
## 210 1,2,3-propanetricarboxylic acid HMDB31193 73.0000 15.657182 11000000
## 32 tryptophan HMDB00929 203.0819 1.352400 76200
## 4 n-octadecanoic acid HMDB00827 283.2634 9.952400 3250000
## 5 myristic acid HMDB00806 227.2009 6.860767 578000
## 6 glycolithocholic acid HMDB00698 432.3107 3.420900 971
## 7 3-indolelactic acid HMDB00671 203.0000 21.233082 37100
## 8 fructose HMDB00660 103.0000 16.349850 789000
## 9 phenylpyruvic acid HMDB00205 165.0545 3.521883 12600
## 10 formononetin glucuronide HMDB41735 445.1206 10.2335500 <NA>
## 11 gancaonin V HMDB37586 311.1301 2.2231667 <NA>
## 12 isoquercitrin HMDB37362 463.0988 2.0986452 <NA>
## 13 ceanothic acid HMDB36851 485.3250 3.4732833 <NA>
## 14 ganoderic acid H HMDB35987 571.2883 3.5425833 <NA>
## 15 isoformononetin HMDB33994 269.0809 2.4982167 <NA>
## 16 liquiritin HMDB29520 417.1239 2.1398795 <NA>
## 17 formononetin HMDB05808 267.0631 3.1570558 <NA>
## 18 trigonelline HMDB00875 136.0404 2.5085333 <NA>
## 19 histamine HMDB00870 112.0763 0.7084167 <NA>
## 20 phytanic acid HMDB00801 311.2948 10.8229833 <NA>
## 21 cholesterol sulfate HMDB00653 465.3041 6.6551167 <NA>
## 22 cytosine HMDB00630 110.0349 9.7993333 <NA>
## 23 erythronic acid HMDB00613 135.0293 0.5236500 <NA>
## 24 chenodeoxycholic acid HMDB00518 391.2845 3.9222000 <NA>
## 25 2-aminobutyric acid HMDB00452 104.0545 0.7084167 <NA>
## 26 2-pyrocatechuic acid HMDB00397 153.0187 2.4666167 <NA>
## 27 urea HMDB00294 100.0000 7.1697798 <NA>
## 28 octadecanamide HMDB34146 284.2946 8.871300 119000
## 29 heptadecanoic acid HMDB02259 269.2477 9.555900 89700
## 30 phosphoric acid HMDB02142 98.9846 4.382100 4440
## 31 hyodeoxycholic acid HMDB00733 391.2842 3.574000 33500
## X0.2 X0.3 X0.4 X0.5 X0.6 X0.7 X0.8
## 1 1 1 1 1 2 2 2
## 2 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0
## 110 5080 4770 4080 2.74e+03 4990 4430 4150
## 210 10100000 10900000 14500000 1.38e+07 13200000 11800000 12300000
## 32 101000 125000 96100 1.18e+05 87900 101000 115000
## 4 2860000 3110000 2160000 2.79e+06 3250000 1610000 2030000
## 5 570000 425000 289000 4.08e+05 603000 168000 346000
## 6 971 971 971 5.09e+00 971 971 971
## 7 69200 123000 69200 9.88e+04 61100 44700 69200
## 8 471000 412000 520000 3.27e+05 603000 432000 558000
## 9 13600 20100 19100 1.93e+04 16300 19500 21000
## 10 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 11 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 12 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 14 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 15 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 16 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 17 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 18 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 19 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 20 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 21 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 22 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 23 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 24 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 25 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 26 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 27 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 28 99100 159000 264000 9.54e+04 361000 361000 267000
## 29 89700 86800 42800 7.08e+04 68400 28100 34600
## 30 3690 3220 4320 4.07e+03 4440 5010 4290
## 31 9930 22200 13300 2.57e+04 7800 24600 33500
## X0.9 X0.10 X1.1 X1.2 X1.3 X1.4 X1.5
## 1 2 2 1 1 1 1 1
## 2 0 0 1 1 1 1 1
## 3 0 0 0.083 0.083 0.083 0.083 0.083
## 110 3540 3310 3.72e+03 1.62e+03 2.91e+03 4.73e+03 3.78e+03
## 210 10400000 13400000 1.25e+07 1.63e+07 9.99e+06 1.54e+07 1.82e+07
## 32 106000 105000 7.24e+04 9.80e+04 1.14e+05 9.10e+04 9.62e+04
## 4 2970000 2840000 4.40e+06 4.36e+06 4.23e+06 2.24e+06 2.42e+06
## 5 442000 587000 3.78e+05 7.13e+05 7.07e+05 3.12e+05 4.87e+05
## 6 971 971 3.10e+01 4.79e+00 2.82e+02 2.82e+02 2.82e+02
## 7 100000 19500 3.73e+04 8.52e+04 4.87e+04 4.87e+04 3.79e+04
## 8 469000 637000 6.77e+05 5.22e+05 6.87e+05 2.88e+05 9.63e+05
## 9 17300 21900 1.04e+04 1.42e+04 1.96e+04 1.79e+04 1.35e+04
## 10 <NA> <NA> 8.55e+02 7.07e+02 8.55e+02 1.76e+02 3.57e+02
## 11 <NA> <NA> 8.76e+04 8.54e+03 3.52e+04 3.11e+04 2.95e+04
## 12 <NA> <NA> 2.17e+03 2.68e+03 2.28e+03 2.71e+03 2.25e+03
## 13 <NA> <NA> 3.12e+00 1.47e+02 1.77e+02 1.77e+02 1.47e+02
## 14 <NA> <NA> 3.27e+06 4.61e+06 2.24e+06 3.41e+06 2.83e+06
## 15 <NA> <NA> 3.90e+02 7.76e+02 1.60e+02 1.37e+02 2.29e+02
## 16 <NA> <NA> 6.15e-01 6.15e-01 6.18e-01 8.72e-01 6.15e-01
## 17 <NA> <NA> 1.50e+01 2.93e+00 5.09e+00 1.33e+00 1.38e+00
## 18 <NA> <NA> 9.69e+02 1.03e+03 1.41e+03 1.31e+03 1.76e+03
## 19 <NA> <NA> 4.82e-01 1.98e+02 1.10e+02 1.88e+01 1.10e+02
## 20 <NA> <NA> 3.92e+04 3.92e+04 2.50e+04 5.45e+03 2.11e+04
## 21 <NA> <NA> 1.30e+05 1.75e+05 1.61e+05 1.46e+05 8.07e+04
## 22 <NA> <NA> 4.63e+04 4.45e+04 4.23e+04 3.75e+04 3.98e+04
## 23 <NA> <NA> 2.03e+02 7.88e+02 2.11e+03 1.58e+03 1.31e+03
## 24 <NA> <NA> 9.69e+02 1.03e+03 1.41e+03 1.31e+03 1.76e+03
## 25 <NA> <NA> 4.82e-01 1.98e+02 1.10e+02 1.88e+01 1.10e+02
## 26 <NA> <NA> 3.92e+04 3.92e+04 2.50e+04 5.45e+03 2.11e+04
## 27 <NA> <NA> 8.89e+02 4.24e+02 5.17e+02 8.45e+02 5.30e+02
## 28 282000 161000 <NA> <NA> <NA> <NA> <NA>
## 29 72100 65200 <NA> <NA> <NA> <NA> <NA>
## 30 2840 3330 <NA> <NA> <NA> <NA> <NA>
## 31 20500 8550 <NA> <NA> <NA> <NA> <NA>
## X1.6 X1.7 X1.8 X1.9 X1.10 X2.1 X2.2
## 1 2 2 2 2 2 1 1
## 2 1 1 1 1 1 2 2
## 3 0.083 0.083 0.083 0.083 0.083 0.25 0.25
## 110 1.90e+03 2.83e+03 2.99e+03 2.83e+03 4.35e+03 3.03e+03 3.86e+03
## 210 1.27e+07 1.24e+07 1.13e+07 1.30e+07 1.36e+07 1.16e+07 1.95e+07
## 32 6.97e+04 8.07e+04 8.15e+04 8.88e+04 8.16e+04 9.26e+04 1.05e+05
## 4 2.65e+06 1.81e+06 2.30e+06 3.26e+06 2.92e+06 4.40e+06 4.39e+06
## 5 4.55e+05 3.13e+05 5.13e+05 4.74e+05 4.23e+05 3.98e+05 7.13e+05
## 6 2.82e+02 1.23e+02 2.82e+02 6.10e+02 6.41e+02 1.68e+01 6.44e+02
## 7 4.87e+04 8.76e+04 2.05e+04 2.37e+04 4.87e+04 4.33e+04 1.12e+05
## 8 7.76e+05 6.27e+05 6.86e+05 5.23e+05 6.91e+05 1.90e+06 8.99e+05
## 9 1.41e+04 1.49e+04 1.62e+04 1.10e+04 1.64e+04 1.29e+04 1.43e+04
## 10 8.55e+02 8.76e+02 8.55e+02 2.16e+03 8.55e+02 6.99e+02 2.00e+03
## 11 3.76e+03 1.88e+04 4.66e+04 7.72e+04 1.13e+04 8.88e+04 7.52e+03
## 12 2.25e+03 2.03e+03 1.91e+03 1.98e+03 2.13e+03 1.32e+03 2.19e+03
## 13 8.88e+01 1.47e+02 1.47e+02 1.47e+02 7.38e+01 1.34e+02 1.34e+02
## 14 3.59e+06 3.20e+06 1.91e+06 3.86e+06 3.21e+06 8.83e+05 1.04e+06
## 15 5.76e+01 3.28e+02 2.64e+02 3.08e+01 2.64e+02 2.79e+02 5.40e+02
## 16 6.15e-01 6.15e-01 6.15e-01 3.56e-01 6.15e-01 2.15e-01 1.23e+00
## 17 5.77e+00 2.29e+00 3.72e+00 3.68e+00 1.69e+00 4.14e+01 2.35e+01
## 18 1.07e+03 5.85e+02 1.24e+03 1.23e+03 9.00e+02 9.47e+02 1.75e+03
## 19 1.98e+02 2.68e+01 1.10e+02 1.40e+02 1.90e+02 2.07e+02 2.55e+02
## 20 1.27e+04 5.83e+03 1.35e+04 9.84e+03 1.29e+04 3.92e+04 3.92e+04
## 21 5.02e+04 4.89e+04 7.98e+04 7.27e+04 1.16e+05 1.99e+05 2.39e+05
## 22 4.22e+04 3.91e+04 3.72e+04 4.47e+04 4.47e+04 4.41e+04 4.84e+04
## 23 2.50e+03 8.93e+02 1.20e+03 1.40e+03 1.14e+03 2.23e+02 5.55e+02
## 24 1.07e+03 5.85e+02 1.24e+03 1.23e+03 9.00e+02 9.47e+02 1.75e+03
## 25 1.98e+02 2.68e+01 1.10e+02 1.40e+02 1.90e+02 2.06e+03 1.26e+03
## 26 1.27e+04 5.83e+03 1.35e+04 9.84e+03 1.29e+04 3.92e+04 3.92e+04
## 27 7.57e+02 3.74e+02 6.74e+02 5.25e+01 1.04e+02 8.30e+01 6.13e+02
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X2.3 X2.4 X2.5 X2.6 X2.7 X2.8 X2.9
## 1 1 1 1 2 2 2 2
## 2 2 2 2 2 2 2 2
## 3 0.25 0.25 0.25 0.25 0.25 0.25 0.25
## 110 3.88e+03 4.29e+03 2.72e+03 4.11e+03 4.40e+03 2.93e+03 4.93e+03
## 210 1.48e+07 1.73e+07 1.63e+07 1.45e+07 1.57e+07 9.90e+06 1.43e+07
## 32 1.14e+05 8.09e+04 9.45e+04 7.31e+04 8.94e+04 7.80e+04 8.05e+04
## 4 3.87e+06 2.46e+06 2.79e+06 3.25e+06 1.79e+06 2.99e+06 3.31e+06
## 5 7.13e+05 3.55e+05 5.26e+05 5.70e+05 2.71e+05 5.22e+05 4.02e+05
## 6 9.82e+02 9.82e+02 2.24e+00 9.82e+02 3.38e+02 9.82e+02 1.65e+03
## 7 4.33e+04 1.14e+04 2.84e+04 4.33e+04 4.33e+04 4.33e+04 2.19e+04
## 8 1.90e+06 1.85e+06 1.13e+06 1.90e+06 1.29e+06 1.54e+06 1.06e+06
## 9 1.96e+04 1.53e+04 1.38e+04 1.34e+04 1.62e+04 1.25e+04 1.34e+04
## 10 6.56e+02 3.11e+03 3.11e+03 2.27e+03 2.27e+03 3.42e+02 4.51e+02
## 11 4.43e+04 3.00e+04 2.25e+04 6.20e+02 1.66e+04 3.93e+04 1.71e+04
## 12 2.43e+03 1.79e+03 1.96e+03 1.87e+03 1.26e+03 1.68e+03 1.57e+03
## 13 1.77e+02 1.51e+02 7.83e+01 1.34e+02 1.25e+02 1.34e+02 4.22e+00
## 14 2.65e+06 1.06e+06 9.35e+05 1.05e+06 1.10e+06 9.60e+05 1.20e+06
## 15 8.10e+02 8.50e+02 3.78e+02 8.50e+02 8.50e+02 4.03e+02 1.98e+02
## 16 5.04e-01 9.23e-01 7.42e-01 9.23e-01 1.29e+00 1.29e+00 7.61e-01
## 17 3.63e+01 2.38e+01 3.35e+01 4.12e+01 1.78e+01 1.99e+01 6.45e+00
## 18 9.51e+02 4.83e+02 1.40e+03 9.44e+02 1.21e+03 1.20e+03 1.04e+03
## 19 2.95e+00 2.07e+02 2.55e+02 1.39e+01 2.07e+02 2.07e+02 2.55e+02
## 20 2.86e+04 8.93e+03 2.26e+04 1.86e+04 1.12e+04 1.33e+04 1.30e+04
## 21 1.71e+05 1.82e+05 1.04e+05 8.03e+04 7.16e+04 9.96e+04 8.52e+04
## 22 4.36e+04 4.83e+04 4.88e+04 4.33e+04 4.51e+04 4.29e+04 4.90e+04
## 23 3.28e+02 1.21e+03 1.55e+02 1.83e+03 9.80e+02 1.29e+03 9.43e+02
## 24 9.51e+02 4.83e+02 1.40e+03 9.44e+02 1.21e+03 1.20e+03 1.04e+03
## 25 2.11e+03 2.21e+03 9.55e+02 1.01e+03 2.06e+03 2.21e+03 1.26e+03
## 26 2.86e+04 8.93e+03 2.26e+04 1.86e+04 1.12e+04 1.33e+04 1.30e+04
## 27 4.09e+02 5.89e+02 8.22e+02 5.74e+02 2.11e+02 7.36e+02 7.08e+01
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X2.10 X3.1 X3.2 X3.3 X3.4 X3.5 X3.6
## 1 2 1 1 1 1 1 2
## 2 2 3 3 3 3 3 3
## 3 0.25 0.5 0.5 0.5 0.5 0.5 0.5
## 110 4.61e+03 4.21e+03 2.38e+03 2.34e+03 3.53e+03 3.72e+03 3.87e+03
## 210 1.34e+07 1.21e+07 1.61e+07 1.15e+07 1.40e+07 1.48e+07 1.33e+07
## 32 8.63e+04 6.84e+04 9.01e+04 9.01e+04 8.44e+04 9.42e+04 6.03e+04
## 4 2.81e+06 3.58e+06 3.31e+06 2.97e+06 2.25e+06 2.55e+06 2.70e+06
## 5 5.04e+05 2.55e+05 5.46e+05 4.27e+05 2.97e+05 4.33e+05 3.77e+05
## 6 1.65e+03 1.65e+03 1.35e+03 1.65e+03 1.65e+03 1.65e+03 1.65e+03
## 7 4.33e+04 2.36e+04 2.36e+04 2.36e+04 2.36e+04 2.36e+04 2.36e+04
## 8 1.61e+06 1.90e+06 1.90e+06 1.90e+06 1.63e+06 1.49e+06 1.90e+06
## 9 1.57e+04 9.02e+03 1.06e+04 1.65e+04 1.55e+04 1.35e+04 1.18e+04
## 10 6.14e+02 1.25e+03 6.10e+02 1.25e+03 2.40e+03 5.77e+02 1.25e+03
## 11 2.22e+03 9.09e+04 9.58e+03 1.69e+04 8.23e+03 1.89e+04 2.43e+03
## 12 2.08e+03 1.78e+03 7.96e+02 1.52e+03 1.81e+03 1.60e+03 1.67e+03
## 13 1.34e+02 1.29e+02 1.25e+02 1.58e+02 1.29e+02 6.32e+01 1.77e+02
## 14 9.61e+05 7.42e+05 1.24e+06 1.71e+06 7.56e+05 5.44e+05 7.59e+05
## 15 3.98e+02 8.50e+02 8.50e+02 8.50e+02 8.50e+02 8.47e+02 8.50e+02
## 16 1.35e+00 2.71e+00 1.71e+00 2.71e+00 2.71e+00 2.71e+00 2.71e+00
## 17 1.93e+01 7.15e+01 4.83e+01 4.07e+01 3.35e+01 4.56e+01 6.56e+01
## 18 1.23e+03 1.05e+03 1.16e+03 6.99e+02 8.31e+02 1.65e+03 4.19e+02
## 19 2.55e+02 7.86e+01 1.24e+02 1.85e+02 1.40e+02 2.55e+02 2.24e+02
## 20 1.43e+04 3.92e+04 3.23e+04 2.43e+04 7.69e+03 2.01e+04 1.40e+04
## 21 1.27e+05 1.36e+05 1.51e+05 1.41e+05 1.29e+05 9.40e+04 5.56e+04
## 22 4.12e+04 4.73e+04 4.97e+04 5.04e+04 5.19e+04 5.25e+04 5.23e+04
## 23 8.89e+02 9.24e+02 1.35e+03 2.44e+03 1.77e+03 3.63e+02 2.26e+03
## 24 1.23e+03 7.42e+05 1.24e+06 1.71e+06 7.56e+05 5.44e+05 7.59e+05
## 25 2.16e+03 2.35e+04 2.36e+04 3.02e+04 1.74e+04 4.46e+04 1.87e+04
## 26 1.43e+04 1.36e+05 1.76e+05 2.18e+05 1.97e+05 1.80e+05 1.74e+05
## 27 8.26e+02 2.37e+04 2.26e+04 3.33e+04 3.56e+04 2.79e+04 2.60e+04
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X3.7 X3.8 X3.9 X3.10 X4.1 X4.2 X4.3
## 1 2 2 2 2 1 1 1
## 2 3 3 3 3 4 4 4
## 3 0.5 0.5 0.5 0.5 1 1 1
## 110 3.28e+03 2.74e+03 3.39e+03 4.84e+03 2.65e+03 3.45e+03 2.67e+03
## 210 1.36e+07 9.84e+06 1.24e+07 1.38e+07 1.16e+07 1.79e+07 1.20e+07
## 32 8.85e+04 8.19e+04 8.10e+04 8.98e+04 7.34e+04 9.21e+04 1.09e+05
## 4 1.78e+06 2.97e+06 2.89e+06 2.59e+06 2.24e+06 2.16e+06 2.36e+06
## 5 3.52e+05 4.96e+05 3.69e+05 4.55e+05 1.73e+05 2.99e+05 3.26e+05
## 6 1.65e+03 1.65e+03 1.22e+03 1.65e+03 5.71e+02 5.71e+02 5.71e+02
## 7 2.36e+04 2.36e+04 2.08e+04 2.64e+04 1.50e+04 1.50e+04 1.50e+04
## 8 1.66e+06 1.55e+06 7.76e+05 1.90e+06 1.36e+06 1.60e+06 1.34e+06
## 9 1.51e+04 1.56e+04 1.29e+04 1.54e+04 1.11e+04 1.33e+04 1.51e+04
## 10 1.25e+03 1.41e+03 1.00e+03 1.50e+03 1.68e+03 4.62e+02 1.68e+03
## 11 4.50e+03 9.09e+04 1.05e+03 3.03e+03 9.09e+04 3.89e+03 3.10e+04
## 12 1.02e+03 1.42e+03 1.09e+03 2.14e+03 1.42e+03 1.80e+03 1.86e+03
## 13 1.29e+02 5.13e+01 1.29e+02 1.37e+02 1.52e+02 1.42e+02 1.77e+02
## 14 5.60e+05 6.65e+05 1.11e+06 2.41e+06 5.57e+06 4.81e+06 5.57e+06
## 15 5.63e+02 8.50e+02 8.50e+02 8.50e+02 8.50e+02 8.50e+02 6.41e+02
## 16 8.45e-01 2.71e+00 2.71e+00 2.61e+00 2.71e+00 1.68e+00 2.71e+00
## 17 7.15e+01 5.41e+01 5.40e+01 5.01e+01 1.47e+01 1.38e+01 1.37e+01
## 18 1.19e+03 1.48e+03 1.67e+03 1.02e+03 1.10e+03 1.53e+03 1.09e+03
## 19 6.33e+01 1.85e+02 4.30e+00 1.85e+02 1.33e+02 2.55e+02 1.50e+02
## 20 8.20e+03 1.64e+04 1.67e+04 1.06e+04 2.55e+04 2.44e+04 1.66e+04
## 21 6.85e+04 1.04e+05 6.49e+04 9.88e+04 2.20e+05 2.02e+05 1.86e+05
## 22 4.19e+04 4.63e+04 4.95e+04 4.33e+04 4.42e+04 5.08e+04 5.08e+04
## 23 2.60e+03 1.26e+03 1.44e+03 2.16e+03 6.14e+02 2.22e+03 2.91e+03
## 24 5.60e+05 6.65e+05 1.11e+06 2.41e+06 2.41e+06 2.41e+06 2.41e+06
## 25 1.73e+04 2.82e+04 2.30e+04 2.49e+04 2.32e+04 2.28e+04 2.79e+04
## 26 1.99e+05 1.91e+05 1.73e+05 2.05e+05 1.25e+05 2.01e+05 1.94e+05
## 27 3.26e+04 3.49e+04 2.72e+04 3.33e+04 3.19e+04 2.95e+04 3.76e+04
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X4.4 X4.5 X4.6 X4.7 X4.8 X4.9 X4.10
## 1 1 1 2 2 2 2 2
## 2 4 4 4 4 4 4 4
## 3 1 1 1 1 1 1 1
## 110 3.28e+03 4.71e+03 3.01e+03 4.09e+03 3.07e+03 3.32e+03 2.67e+03
## 210 1.53e+07 1.77e+07 1.46e+07 1.33e+07 1.09e+07 1.27e+07 1.37e+07
## 32 8.68e+04 8.13e+04 6.34e+04 6.70e+04 7.90e+04 8.11e+04 7.30e+04
## 4 1.84e+06 1.63e+06 1.77e+06 1.55e+06 3.02e+06 2.32e+06 1.76e+06
## 5 2.40e+05 2.15e+05 2.25e+05 2.21e+05 4.69e+05 2.79e+05 2.36e+05
## 6 5.71e+02 3.08e+02 5.71e+02 1.31e+02 5.71e+02 2.35e+02 1.61e+03
## 7 1.50e+04 1.50e+04 1.50e+04 1.50e+04 1.50e+04 1.50e+04 1.50e+04
## 8 8.82e+05 1.10e+06 1.48e+06 1.45e+06 1.48e+06 6.17e+05 1.33e+06
## 9 1.73e+04 1.19e+04 1.24e+04 1.16e+04 1.32e+04 1.35e+04 1.37e+04
## 10 6.14e+02 6.40e+02 7.11e+02 3.11e+03 5.53e+02 1.68e+03 4.50e+02
## 11 1.45e+04 5.12e+04 4.70e+04 1.08e+04 7.74e+04 4.09e+04 3.06e+04
## 12 1.61e+03 1.70e+03 1.89e+03 1.54e+03 9.78e+02 8.86e+02 1.27e+03
## 13 1.08e+02 6.62e+01 1.42e+02 4.03e+01 1.42e+02 1.52e+02 1.42e+02
## 14 4.76e+06 2.11e+06 1.09e+06 1.78e+06 2.18e+06 4.74e+06 1.06e+06
## 15 8.50e+02 7.45e+02 6.70e+02 8.50e+02 8.50e+02 8.50e+02 8.50e+02
## 16 2.71e+00 2.71e+00 2.71e+00 2.71e+00 2.71e+00 2.01e+00 2.71e+00
## 17 1.49e+01 8.77e+00 6.58e+00 3.45e+01 3.24e+01 1.20e+01 1.86e+01
## 18 1.47e+03 8.11e+02 8.69e+02 1.51e+03 1.29e+03 1.28e+03 1.25e+03
## 19 1.50e+02 1.09e+02 2.55e+02 1.40e+02 2.15e+01 8.68e+01 1.82e+02
## 20 8.79e+03 1.13e+04 3.64e+03 1.01e+04 1.77e+04 9.52e+03 1.06e+04
## 21 1.89e+05 9.95e+04 7.83e+04 6.57e+04 1.11e+05 7.89e+04 1.19e+05
## 22 4.80e+04 5.19e+04 4.90e+04 4.39e+04 4.44e+04 5.17e+04 4.72e+04
## 23 2.91e+03 1.58e+02 2.91e+03 1.71e+03 1.43e+03 2.04e+03 8.41e+02
## 24 1.17e+06 1.23e+06 1.01e+06 1.04e+06 2.24e+06 2.41e+06 2.41e+06
## 25 2.21e+04 4.15e+04 1.71e+04 1.54e+04 2.80e+04 2.60e+04 2.16e+04
## 26 1.85e+05 1.77e+05 1.73e+05 1.88e+05 1.78e+05 1.66e+05 1.98e+05
## 27 3.46e+04 2.64e+04 3.16e+04 3.71e+04 3.67e+04 3.63e+04 4.31e+04
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X5.1 X5.2 X5.3 X5.4 X5.5 X5.6 X5.7
## 1 1 1 1 1 1 2 2
## 2 5 5 5 5 5 5 5
## 3 2 2 2 2 2 2 2
## 110 3.63e+03 2.50e+03 1.76e+03 2.56e+03 2.81e+03 1.15e+03 2.93e+03
## 210 1.29e+07 1.59e+07 1.27e+07 1.57e+07 1.74e+07 9.80e+06 1.29e+07
## 32 6.51e+04 7.04e+04 8.74e+04 6.86e+04 7.87e+04 4.52e+04 7.71e+04
## 4 2.45e+06 2.03e+06 3.25e+06 2.19e+06 2.43e+06 2.04e+06 1.69e+06
## 5 2.36e+05 3.13e+05 5.74e+05 3.02e+05 3.98e+05 2.69e+05 2.42e+05
## 6 1.81e+02 5.87e+02 1.17e+03 1.74e+01 1.17e+03 1.17e+03 1.17e+03
## 7 1.11e+05 1.11e+05 1.11e+05 1.11e+05 1.11e+05 1.11e+05 1.11e+05
## 8 5.01e+05 4.58e+05 4.13e+05 3.37e+05 3.62e+05 2.88e+05 2.94e+05
## 9 9.34e+03 1.07e+04 1.52e+04 1.59e+04 1.23e+04 9.96e+03 1.38e+04
## 10 3.77e+02 4.21e+02 1.58e+03 3.11e+03 2.48e+03 1.44e+03 2.48e+03
## 11 1.44e+03 1.65e+03 1.85e+03 1.14e+03 1.45e+03 1.22e+03 1.45e+03
## 12 1.13e+02 1.62e+02 1.08e+02 1.69e+02 2.70e+01 2.48e+01 3.22e+01
## 13 7.50e+01 9.20e+01 1.23e+02 7.60e+01 1.77e+02 8.80e+01 1.77e+02
## 14 1.69e+04 1.21e+04 1.54e+04 1.51e+04 2.83e+04 1.10e+04 1.74e+04
## 15 4.09e+02 3.75e+02 9.18e+01 4.09e+02 9.30e+01 1.81e+02 4.09e+02
## 16 2.71e+00 2.21e+00 2.71e+00 2.71e+00 2.71e+00 2.71e+00 2.71e+00
## 17 1.57e+00 1.12e+00 5.93e+00 4.70e-01 2.25e+00 2.42e+00 3.24e+00
## 18 1.09e+03 1.12e+03 1.43e+03 1.61e+03 7.71e+02 8.01e+02 1.47e+03
## 19 1.15e+02 7.61e+00 8.39e-01 1.02e+02 5.27e+01 1.16e+02 9.80e+01
## 20 2.37e+04 1.45e+04 1.72e+04 1.06e+04 1.91e+04 9.62e+03 1.26e+04
## 21 2.02e+05 1.90e+05 1.85e+05 1.94e+05 1.16e+05 5.55e+04 7.96e+04
## 22 4.42e+04 5.17e+04 5.17e+04 5.13e+04 5.24e+04 5.26e+04 4.30e+04
## 23 5.17e+02 1.66e+03 1.59e+03 1.74e+03 3.37e+02 3.03e+02 2.03e+03
## 24 7.07e+04 3.32e+04 2.41e+04 1.45e+04 2.59e+04 1.46e+03 5.03e+04
## 25 1.44e+03 1.65e+03 1.85e+03 1.14e+03 1.45e+03 1.22e+03 1.45e+03
## 26 1.13e+02 1.62e+02 1.08e+02 1.69e+02 2.70e+01 2.48e+01 3.22e+01
## 27 4.31e+04 4.31e+04 4.31e+04 4.31e+04 4.31e+04 4.31e+04 4.31e+04
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X5.8 X5.9 X5.10
## 1 2 2 2
## 2 5 5 5
## 3 2 2 2
## 110 2.84e+03 2.27e+03 2.13e+03
## 210 1.35e+07 1.16e+07 1.54e+07
## 32 7.77e+04 7.38e+04 7.11e+04
## 4 2.94e+06 1.96e+06 1.88e+06
## 5 5.11e+05 2.14e+05 3.20e+05
## 6 1.17e+03 1.17e+03 1.65e+03
## 7 1.22e+05 1.11e+05 9.97e+04
## 8 6.43e+05 3.77e+05 3.37e+05
## 9 1.13e+04 1.19e+04 1.34e+04
## 10 1.47e+03 5.91e+02 2.48e+03
## 11 9.35e+02 9.08e+02 1.19e+03
## 12 2.38e+02 1.36e+02 1.13e+02
## 13 9.70e+01 9.90e+01 1.02e+02
## 14 4.33e+04 1.58e+04 1.58e+04
## 15 8.50e+02 1.88e+02 8.50e+02
## 16 9.90e-01 2.71e+00 2.71e+00
## 17 5.81e+00 4.47e+00 3.27e+00
## 18 1.18e+03 9.28e+02 1.02e+03
## 19 7.31e+01 7.31e+01 9.24e+01
## 20 1.66e+04 8.01e+03 8.55e+03
## 21 1.10e+05 7.94e+04 1.13e+05
## 22 4.83e+04 5.08e+04 4.68e+04
## 23 1.44e+03 1.62e+03 8.24e+02
## 24 1.03e+05 6.59e+03 2.69e+04
## 25 9.35e+02 9.08e+02 1.19e+03
## 26 2.38e+02 1.36e+02 1.13e+02
## 27 4.31e+04 4.31e+04 4.31e+04
## 28 <NA> <NA> <NA>
## 29 <NA> <NA> <NA>
## 30 <NA> <NA> <NA>
## 31 <NA> <NA> <NA>An example of the differential compounds, with original data:
orgA<-dif$A_pre
as.data.frame(orgA)## Name ID m.z RT.min. X0.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 0
## 3 timepoints(h) <NA> <NA> 0
## 110 octanoyl-rac-glycerol inx0001 219.1401 3.5638 4180
## 210 1,2,3-propanetricarboxylic acid HMDB31193 73 15.657182 1.1e+07
## 32 tryptophan HMDB00929 203.0819 1.3524 76200
## 4 n-octadecanoic acid HMDB00827 283.2634 9.9524 3250000
## 5 myristic acid HMDB00806 227.2009 6.8607667 578000
## 6 glycolithocholic acid HMDB00698 432.3107 3.4209 971
## 7 3-indolelactic acid HMDB00671 203 21.2330824 37100
## 8 fructose HMDB00660 103 16.3498505 789000
## 9 phenylpyruvic acid HMDB00205 165.0545 3.5218833 12600
## 10 formononetin glucuronide HMDB41735 445.12059 10.23355 <NA>
## 11 gancaonin V HMDB37586 311.13009 2.2231667 <NA>
## 12 isoquercitrin HMDB37362 463.0988 2.0986452 <NA>
## 13 ceanothic acid HMDB36851 485.32502 3.4732833 <NA>
## 14 ganoderic acid H HMDB35987 571.28834 3.5425833 <NA>
## 15 isoformononetin HMDB33994 269.08095 2.4982167 <NA>
## 16 liquiritin HMDB29520 417.1239 2.1398795 <NA>
## 17 formononetin HMDB05808 267.0631 3.1570558 <NA>
## 18 trigonelline HMDB00875 136.04045 2.5085333 <NA>
## 19 histamine HMDB00870 112.07626 0.7084167 <NA>
## 20 phytanic acid HMDB00801 311.29478 10.8229833 <NA>
## 21 cholesterol sulfate HMDB00653 465.30412 6.6551167 <NA>
## 22 cytosine HMDB00630 110.03495 9.7993333 <NA>
## 23 erythronic acid HMDB00613 135.02929 0.52365 <NA>
## 24 chenodeoxycholic acid HMDB00518 391.28446 3.9222 <NA>
## 25 2-aminobutyric acid HMDB00452 104.05447 0.7084167 <NA>
## 26 2-pyrocatechuic acid HMDB00397 153.01865 2.4666167 <NA>
## 27 urea HMDB00294 100 7.1697798 <NA>
## 28 octadecanamide HMDB34146 284.2946 8.8713 119000
## 29 heptadecanoic acid HMDB02259 269.2477 9.5559 89700
## 30 phosphoric acid HMDB02142 98.9846 4.3821 4440
## 31 hyodeoxycholic acid HMDB00733 391.2842 3.574 33500
## X0.2 X0.3 X0.4 X0.5 X0.6 X0.7 X0.8
## 1 1 1 1 1 2 2 2
## 2 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0
## 110 5080 4770 4080 2740 4990 4430 4150
## 210 10100000 10900000 14500000 13800000 13200000 11800000 12300000
## 32 101000 125000 96100 118000 87900 101000 115000
## 4 2860000 3110000 2160000 2790000 3250000 1610000 2030000
## 5 570000 425000 289000 408000 603000 168000 346000
## 6 971 971 971 5.09 971 971 971
## 7 69200 123000 69200 98800 61100 44700 69200
## 8 471000 412000 520000 327000 603000 432000 558000
## 9 13600 20100 19100 19300 16300 19500 21000
## 10 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 11 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 12 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 14 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 15 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 16 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 17 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 18 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 19 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 20 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 21 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 22 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 23 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 24 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 25 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 26 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 27 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 28 99100 159000 264000 95400 361000 361000 267000
## 29 89700 86800 42800 70800 68400 28100 34600
## 30 3690 3220 4320 4070 4440 5010 4290
## 31 9930 22200 13300 25700 7800 24600 33500
## X0.9 X0.10 X1.1 X1.2 X1.3 X1.4 X1.5 X1.6
## 1 2 2 1 1 1 1 1 2
## 2 0 0 1 1 1 1 1 1
## 3 0 0 0.083 0.083 0.083 0.083 0.083 0.083
## 110 3540 3310 3720 1620 2910 4730 3780 1900
## 210 10400000 13400000 12500000 16300000 9990000 15400000 18200000 12700000
## 32 106000 105000 72400 98000 132000 91000 96200 69700
## 4 2970000 2840000 4400000 4360000 4230000 2240000 2420000 2650000
## 5 442000 587000 378000 713000 707000 312000 487000 455000
## 6 971 971 31 4.79 282 282 282 282
## 7 1e+05 19500 37300 85200 48700 48700 37900 48700
## 8 469000 637000 677000 522000 687000 0 963000 776000
## 9 17300 21900 10400 14200 22400 17900 13500 14100
## 10 <NA> <NA> 855 707 855 176 357 855
## 11 <NA> <NA> 87600 8540 35200 31100 29500 3760
## 12 <NA> <NA> 2170 2680 2280 2710 2250 2250
## 13 <NA> <NA> 3.12 147 238 238 147 88.8
## 14 <NA> <NA> 3270000 4610000 2240000 3410000 2830000 3590000
## 15 <NA> <NA> 390 776 160 137 229 57.6
## 16 <NA> <NA> 0.615 0.615 0.618 0.872 0.615 0.615
## 17 <NA> <NA> 15 2.93 5.09 1.33 1.38 5.77
## 18 <NA> <NA> 969 1030 1410 1310 1760 1070
## 19 <NA> <NA> 0.482 198 110 18.8 110 198
## 20 <NA> <NA> 39200 39200 25000 5450 21100 12700
## 21 <NA> <NA> 130000 175000 161000 146000 80700 50200
## 22 <NA> <NA> 46300 44500 42300 37500 39800 42200
## 23 <NA> <NA> 203 788 2110 1580 1310 2500
## 24 <NA> <NA> 969 1030 1410 1310 1760 1070
## 25 <NA> <NA> 0.482 198 110 18.8 110 198
## 26 <NA> <NA> 39200 39200 25000 5450 21100 12700
## 27 <NA> <NA> 889 424 517 845 530 757
## 28 282000 161000 <NA> <NA> <NA> <NA> <NA> <NA>
## 29 72100 65200 <NA> <NA> <NA> <NA> <NA> <NA>
## 30 2840 3330 <NA> <NA> <NA> <NA> <NA> <NA>
## 31 20500 8550 <NA> <NA> <NA> <NA> <NA> <NA>
## X1.7 X1.8 X1.9 X1.10 X2.1 X2.2 X2.3 X2.4
## 1 2 2 2 2 1 1 1 1
## 2 1 1 1 1 2 2 2 2
## 3 0.083 0.083 0.083 0.083 0.25 0.25 0.25 0.25
## 110 2830 2990 2830 4350 3030 3860 3880 4290
## 210 12400000 11300000 1.3e+07 13600000 11600000 19500000 14800000 17300000
## 32 80700 81500 88800 81600 92600 105000 114000 80900
## 4 1810000 2300000 3260000 2920000 4620000 4390000 3870000 2460000
## 5 313000 513000 474000 423000 398000 713000 713000 355000
## 6 123 282 610 641 16.8 644 982 982
## 7 87600 20500 23700 48700 43300 112000 43300 11400
## 8 627000 686000 523000 691000 1900000 899000 1900000 1850000
## 9 14900 16200 11000 16400 12900 14300 19600 15300
## 10 876 855 2160 855 699 2000 656 3110
## 11 18800 46600 77200 11300 88800 7520 44300 30000
## 12 2030 1910 1980 2130 1320 2190 2430 1790
## 13 147 147 147 73.8 134 134 238 151
## 14 3200000 1910000 3860000 3210000 883000 1040000 2650000 1060000
## 15 328 264 30.8 264 279 540 810 850
## 16 0.615 0.615 0.356 0.615 0.215 1.23 0.504 0.923
## 17 2.29 3.72 3.68 1.69 41.4 23.5 36.3 23.8
## 18 585 1240 1230 900 947 1750 951 483
## 19 26.8 110 140 190 207 255 2.95 207
## 20 5830 13500 9840 12900 39200 39200 28600 8930
## 21 48900 79800 72700 116000 199000 239000 171000 182000
## 22 39100 37200 44700 44700 44100 48400 43600 48300
## 23 893 1200 1400 1140 223 555 328 1210
## 24 585 1240 1230 900 947 1750 951 483
## 25 26.8 110 140 190 2060 1260 2110 2210
## 26 5830 13500 9840 12900 39200 39200 28600 8930
## 27 374 674 52.5 104 83 613 409 589
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X2.5 X2.6 X2.7 X2.8 X2.9 X2.10 X3.1 X3.2
## 1 1 2 2 2 2 2 1 1
## 2 2 2 2 2 2 2 3 3
## 3 0.25 0.25 0.25 0.25 0.25 0.25 0.5 0.5
## 110 2720 4110 4400 2930 4930 4610 4210 2380
## 210 16300000 14500000 15700000 9900000 14300000 13400000 12100000 16100000
## 32 94500 73100 89400 78000 80500 86300 68400 90100
## 4 2790000 3250000 1790000 2990000 3310000 2810000 3580000 3310000
## 5 526000 570000 271000 522000 402000 504000 255000 546000
## 6 2.24 982 338 982 1650 3240 3940 1350
## 7 28400 43300 43300 43300 21900 43300 23600 23600
## 8 1130000 1900000 1290000 1540000 1060000 1610000 1900000 1900000
## 9 13800 13400 16200 12500 13400 15700 9020 10600
## 10 3110 2270 2270 342 451 614 1250 610
## 11 22500 620 16600 39300 17100 2220 90900 9580
## 12 1960 1870 1260 1680 1570 2080 1780 796
## 13 78.3 134 125 134 4.22 134 129 125
## 14 935000 1050000 1100000 960000 1200000 961000 742000 1240000
## 15 378 850 850 403 198 398 850 850
## 16 0.742 0.923 1.29 1.29 0.761 1.35 2.71 1.71
## 17 33.5 41.2 17.8 19.9 6.45 19.3 87 48.3
## 18 1400 944 1210 1200 1040 1230 1050 1160
## 19 255 13.9 207 207 255 255 78.6 124
## 20 22600 18600 11200 13300 13000 14300 39200 32300
## 21 104000 80300 71600 99600 85200 127000 136000 151000
## 22 48800 43300 45100 42900 49000 41200 47300 49700
## 23 155 1830 980 1290 943 889 924 1350
## 24 1400 944 1210 1200 1040 1230 742000 1240000
## 25 955 1010 2060 2210 1260 2160 23500 23600
## 26 22600 18600 11200 13300 13000 14300 136000 176000
## 27 822 574 211 736 70.8 826 23700 22600
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X3.3 X3.4 X3.5 X3.6 X3.7 X3.8 X3.9 X3.10
## 1 1 1 1 2 2 2 2 2
## 2 3 3 3 3 3 3 3 3
## 3 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5
## 110 2340 3530 3720 3870 3280 2740 3390 4840
## 210 11500000 1.4e+07 14800000 13300000 13600000 9840000 12400000 13800000
## 32 90100 84400 94200 60300 88500 81900 81000 89800
## 4 2970000 2250000 2550000 2700000 1780000 2970000 2890000 2590000
## 5 427000 297000 433000 377000 352000 496000 369000 455000
## 6 3940 3940 3940 3940 3940 3940 1220 5320
## 7 23600 23600 23600 23600 23600 23600 20800 26400
## 8 1900000 1630000 1490000 1900000 1660000 1550000 776000 1900000
## 9 16500 15500 13500 11800 15100 15600 12900 15400
## 10 1250 2400 577 1250 1250 1410 1000 1500
## 11 16900 8230 18900 2430 4500 103000 1050 3030
## 12 1520 1810 1600 1670 1020 1420 1090 2140
## 13 158 129 63.2 238 129 51.3 129 137
## 14 1710000 756000 544000 759000 560000 665000 1110000 2410000
## 15 850 850 847 850 563 850 850 850
## 16 2.71 2.71 2.71 2.71 0.845 2.71 2.71 2.61
## 17 40.7 33.5 45.6 65.6 71.5 54.1 54 50.1
## 18 699 831 1650 419 1190 1480 1670 1020
## 19 185 140 255 224 63.3 185 4.3 185
## 20 24300 7690 20100 14000 8200 16400 16700 10600
## 21 141000 129000 94000 55600 68500 104000 64900 98800
## 22 50400 51900 52500 52300 41900 46300 49500 43300
## 23 2440 1770 363 2260 2600 1260 1440 2160
## 24 1710000 756000 544000 759000 560000 665000 1110000 2410000
## 25 30200 17400 44600 18700 17300 28200 23000 24900
## 26 218000 197000 180000 174000 199000 191000 173000 205000
## 27 33300 35600 27900 26000 32600 34900 27200 33300
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X4.1 X4.2 X4.3 X4.4 X4.5 X4.6 X4.7 X4.8
## 1 1 1 1 1 1 2 2 2
## 2 4 4 4 4 4 4 4 4
## 3 1 1 1 1 1 1 1 1
## 110 2650 3450 2670 3280 4710 3010 4090 3070
## 210 11600000 17900000 1.2e+07 15300000 17700000 14600000 13300000 10900000
## 32 73400 92100 109000 86800 81300 63400 67000 79000
## 4 2240000 2160000 2360000 1840000 1630000 1770000 1550000 3020000
## 5 173000 299000 326000 240000 215000 225000 221000 469000
## 6 571 571 571 571 308 571 131 571
## 7 15000 15000 15000 15000 15000 15000 15000 15000
## 8 1360000 1600000 1340000 882000 1100000 1480000 1450000 1480000
## 9 11100 13300 15100 17300 11900 12400 11600 13200
## 10 1680 462 1680 614 640 711 3110 553
## 11 103000 3890 31000 14500 51200 47000 10800 77400
## 12 1420 1800 1860 1610 1700 1890 1540 978
## 13 152 142 238 108 66.2 142 40.3 142
## 14 5570000 4810000 5570000 4760000 2110000 1090000 1780000 2180000
## 15 850 850 641 850 745 670 850 850
## 16 2.71 1.68 2.71 2.71 2.71 2.71 2.71 2.71
## 17 14.7 13.8 13.7 14.9 8.77 6.58 34.5 32.4
## 18 1100 1530 1090 1470 811 869 1510 1290
## 19 133 255 150 150 109 255 140 21.5
## 20 25500 24400 16600 8790 11300 3640 10100 17700
## 21 220000 202000 186000 189000 99500 78300 65700 111000
## 22 44200 50800 50800 48000 51900 49000 43900 44400
## 23 614 2220 2910 2910 158 2910 1710 1430
## 24 2930000 2980000 2780000 1170000 1230000 1010000 1040000 2240000
## 25 23200 22800 27900 22100 41500 17100 15400 28000
## 26 125000 201000 194000 185000 177000 173000 188000 178000
## 27 31900 29500 37600 34600 26400 31600 37100 36700
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X4.9 X4.10 X5.1 X5.2 X5.3 X5.4 X5.5 X5.6
## 1 2 2 1 1 1 1 1 2
## 2 4 4 5 5 5 5 5 5
## 3 1 1 2 2 2 2 2 2
## 110 3320 2670 3630 2500 1760 2560 2810 1150
## 210 12700000 13700000 12900000 15900000 12700000 15700000 17400000 9800000
## 32 81100 73000 65100 70400 87400 68600 78700 45200
## 4 2320000 1760000 2450000 2030000 3250000 2190000 2430000 2040000
## 5 279000 236000 236000 313000 574000 302000 398000 269000
## 6 235 1610 181 587 1170 17.4 1170 1170
## 7 15000 15000 111000 111000 111000 111000 111000 111000
## 8 617000 1330000 501000 458000 413000 337000 362000 288000
## 9 13500 13700 9340 10700 15200 15900 12300 9960
## 10 1680 450 377 421 1580 3110 2480 1440
## 11 40900 30600 1440 1650 1850 1140 1450 1220
## 12 886 1270 113 162 108 169 27 24.8
## 13 152 142 75 92 123 76 1150000 88
## 14 4740000 1060000 16900 12100 15400 15100 28300 11000
## 15 850 850 409 375 91.8 409 93 181
## 16 2.01 2.71 2.71 2.21 2.71 2.71 2.71 2.71
## 17 12 18.6 1.57 1.12 5.93 0.47 2.25 2.42
## 18 1280 1250 1090 1120 1430 1610 771 801
## 19 86.8 182 115 7.61 0.839 102 52.7 116
## 20 9520 10600 23700 14500 17200 10600 19100 9620
## 21 78900 119000 202000 190000 185000 194000 116000 55500
## 22 51700 47200 44200 51700 51700 51300 52400 52600
## 23 2040 841 517 1660 1590 1740 337 303
## 24 3090000 4280000 70700 33200 24100 14500 25900 1460
## 25 26000 21600 1440 1650 1850 1140 1450 1220
## 26 166000 198000 113 162 108 169 27 24.8
## 27 36300 43100 1780000 2930000 2930000 769000 1150000 3500000
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X5.7 X5.8 X5.9 X5.10
## 1 2 2 2 2
## 2 5 5 5 5
## 3 2 2 2 2
## 110 2930 2840 2270 2130
## 210 12900000 13500000 11600000 15400000
## 32 77100 77700 73800 71100
## 4 1690000 2940000 1960000 1880000
## 5 242000 511000 214000 320000
## 6 1170 1170 1170 3900
## 7 111000 122000 111000 99700
## 8 294000 643000 377000 337000
## 9 13800 11300 11900 13400
## 10 2480 1470 591 2480
## 11 1450 935 908 1190
## 12 32.2 238 136 113
## 13 177 97 99 102
## 14 17400 43300 15800 15800
## 15 409 850 188 850
## 16 2.71 0.99 2.71 2.71
## 17 3.24 5.81 4.47 3.27
## 18 1470 1180 928 1020
## 19 98 73.1 73.1 92.4
## 20 12600 16600 8010 8550
## 21 79600 110000 79400 113000
## 22 43000 48300 50800 46800
## 23 2030 1440 1620 824
## 24 50300 103000 6590 26900
## 25 1450 935 908 1190
## 26 32.2 238 136 113
## 27 1770000 1520000 998000 2260000
## 28 <NA> <NA> <NA> <NA>
## 29 <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA>
## 31 <NA> <NA> <NA> <NA>The p values:
p<-dif$p
p## [,1] [,2] [,3]
## octanoyl-rac-glycerol 0.0260244164 4.654868e-01 5.919837e-02
## 1,2,3-propanetricarboxylic acid 0.1460157496 2.074242e-02 1.922077e-01
## tryptophan 0.0202897340 3.684567e-02 2.457435e-03
## n-octadecanoic acid 0.3074598184 1.213953e-01 7.680574e-01
## myristic acid 0.5815884996 4.024950e-01 4.600790e-01
## glycolithocholic acid 0.0001194918 8.082684e-01 1.790408e-05
## 3-indolelactic acid 0.1123450519 6.350310e-02 1.309725e-03
## fructose 0.0984948479 1.007318e-05 7.965273e-07
## phenylpyruvic acid 0.0251127544 1.178979e-02 2.273702e-03
## [,4] [,5]
## octanoyl-rac-glycerol 1.721622e-02 6.383351e-05
## 1,2,3-propanetricarboxylic acid 6.119316e-02 7.879574e-02
## tryptophan 1.884732e-03 4.076133e-05
## n-octadecanoic acid 1.369011e-02 1.061509e-01
## myristic acid 5.494115e-03 1.007495e-01
## glycolithocholic acid 7.473468e-02 7.119534e-01
## 3-indolelactic acid 4.042092e-04 2.215191e-03
## fructose 1.293703e-05 3.866770e-02
## phenylpyruvic acid 8.147760e-04 2.044026e-04The adjusted p values:
padj<-dif$p_adj
padj## [,1] [,2] [,3]
## octanoyl-rac-glycerol 0.0509173364 0.5109001872 1.019886e-01
## 1,2,3-propanetricarboxylic acid 0.1825196870 0.0444480340 2.337661e-01
## tryptophan 0.0444480340 0.0690856278 7.372306e-03
## n-octadecanoic acid 0.3640971533 0.1560796964 7.855133e-01
## myristic acid 0.6231305353 0.4644173386 5.109002e-01
## glycolithocholic acid 0.0007681614 0.8082683735 2.014209e-04
## 3-indolelactic acid 0.1486919805 0.1020585555 5.357964e-03
## fructose 0.1416789827 0.0001940554 3.584373e-05
## phenylpyruvic acid 0.0509173364 0.0312082673 7.308328e-03
## [,4] [,5]
## octanoyl-rac-glycerol 0.0407752660 0.0004787513
## 1,2,3-propanetricarboxylic acid 0.1019886063 0.1181936146
## tryptophan 0.0070677432 0.0003668520
## n-octadecanoic acid 0.0342252873 0.1447511932
## myristic acid 0.0154521974 0.1416789827
## glycolithocholic acid 0.1159676132 0.7450674653
## 3-indolelactic acid 0.0020210459 0.0073083285
## fructose 0.0001940554 0.0696018547
## phenylpyruvic acid 0.0036664920 0.0011497647GetEndoA function to get the altered endogenous metabolites by similarity analysis on the list of differential compounds and the list of pre-dose compounds：
data("preData")
data("A")
data("design")
data("simidata")
GetEndo(preData,A,simidata,sim=80,filepath=getwd(),design=FALSE)## Name ID m.z RT.min. X0.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 0
## 3 timepoints(h) <NA> <NA> 0
## 7 octanoyl-rac-glycerol inx0001 219.1401 3.563800 4180
## 28 octadecanamide HMDB34146 284.2946 8.871300 119000
## 8 1,2,3-propanetricarboxylic acid HMDB31193 73.0000 15.657182 11000000
## 29 heptadecanoic acid HMDB02259 269.2477 9.555900 89700
## 30 phosphoric acid HMDB02142 98.9846 4.382100 4440
## 5 tryptophan HMDB00929 203.0819 1.352400 76200
## 4 n-octadecanoic acid HMDB00827 283.2634 9.952400 3250000
## 32 myristic acid HMDB00806 227.2009 6.860767 578000
## 31 hyodeoxycholic acid HMDB00733 391.2842 3.574000 33500
## 110 glycolithocholic acid HMDB00698 432.3107 3.420900 971
## 9 3-indolelactic acid HMDB00671 203.0000 21.233082 37100
## 210 fructose HMDB00660 103.0000 16.349850 789000
## 6 phenylpyruvic acid HMDB00205 165.0545 3.521883 12600
## X0.2 X0.3 X0.4 X0.5 X0.6 X0.7 X0.8
## 1 1 1 1 1 2 2 2
## 2 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0
## 7 5080 4770 4080 2.74e+03 4990 4430 4150
## 28 99100 159000 264000 9.54e+04 361000 361000 267000
## 8 10100000 10900000 14500000 1.38e+07 13200000 11800000 12300000
## 29 89700 86800 42800 7.08e+04 68400 28100 34600
## 30 3690 3220 4320 4.07e+03 4440 5010 4290
## 5 101000 125000 96100 1.18e+05 87900 101000 115000
## 4 2860000 3110000 2160000 2.79e+06 3250000 1610000 2030000
## 32 570000 425000 289000 4.08e+05 603000 168000 346000
## 31 9930 22200 13300 2.57e+04 7800 24600 33500
## 110 971 971 971 5.09e+00 971 971 971
## 9 69200 123000 69200 9.88e+04 61100 44700 69200
## 210 471000 412000 520000 3.27e+05 603000 432000 558000
## 6 13600 20100 19100 1.93e+04 16300 19500 21000
## X0.9 X0.10 X1.1 X1.2 X1.3 X1.4 X1.5
## 1 2 2 1 1 1 1 1
## 2 0 0 1 1 1 1 1
## 3 0 0 0.083 0.083 0.083 0.083 0.083
## 7 3540 3310 3.72e+03 1.62e+03 2.91e+03 4.73e+03 3.78e+03
## 28 282000 161000 <NA> <NA> <NA> <NA> <NA>
## 8 10400000 13400000 1.25e+07 1.63e+07 9.99e+06 1.54e+07 1.82e+07
## 29 72100 65200 <NA> <NA> <NA> <NA> <NA>
## 30 2840 3330 <NA> <NA> <NA> <NA> <NA>
## 5 106000 105000 7.24e+04 9.80e+04 1.14e+05 9.10e+04 9.62e+04
## 4 2970000 2840000 4.40e+06 4.36e+06 4.23e+06 2.24e+06 2.42e+06
## 32 442000 587000 3.78e+05 7.13e+05 7.07e+05 3.12e+05 4.87e+05
## 31 20500 8550 <NA> <NA> <NA> <NA> <NA>
## 110 971 971 3.10e+01 4.79e+00 2.82e+02 2.82e+02 2.82e+02
## 9 100000 19500 3.73e+04 8.52e+04 4.87e+04 4.87e+04 3.79e+04
## 210 469000 637000 6.77e+05 5.22e+05 6.87e+05 2.88e+05 9.63e+05
## 6 17300 21900 1.04e+04 1.42e+04 1.96e+04 1.79e+04 1.35e+04
## X1.6 X1.7 X1.8 X1.9 X1.10 X2.1 X2.2
## 1 2 2 2 2 2 1 1
## 2 1 1 1 1 1 2 2
## 3 0.083 0.083 0.083 0.083 0.083 0.25 0.25
## 7 1.90e+03 2.83e+03 2.99e+03 2.83e+03 4.35e+03 3.03e+03 3.86e+03
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 1.27e+07 1.24e+07 1.13e+07 1.30e+07 1.36e+07 1.16e+07 1.95e+07
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5 6.97e+04 8.07e+04 8.15e+04 8.88e+04 8.16e+04 9.26e+04 1.05e+05
## 4 2.65e+06 1.81e+06 2.30e+06 3.26e+06 2.92e+06 4.40e+06 4.39e+06
## 32 4.55e+05 3.13e+05 5.13e+05 4.74e+05 4.23e+05 3.98e+05 7.13e+05
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 2.82e+02 1.23e+02 2.82e+02 6.10e+02 6.41e+02 1.68e+01 6.44e+02
## 9 4.87e+04 8.76e+04 2.05e+04 2.37e+04 4.87e+04 4.33e+04 1.12e+05
## 210 7.76e+05 6.27e+05 6.86e+05 5.23e+05 6.91e+05 1.90e+06 8.99e+05
## 6 1.41e+04 1.49e+04 1.62e+04 1.10e+04 1.64e+04 1.29e+04 1.43e+04
## X2.3 X2.4 X2.5 X2.6 X2.7 X2.8 X2.9
## 1 1 1 1 2 2 2 2
## 2 2 2 2 2 2 2 2
## 3 0.25 0.25 0.25 0.25 0.25 0.25 0.25
## 7 3.88e+03 4.29e+03 2.72e+03 4.11e+03 4.40e+03 2.93e+03 4.93e+03
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 1.48e+07 1.73e+07 1.63e+07 1.45e+07 1.57e+07 9.90e+06 1.43e+07
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5 1.14e+05 8.09e+04 9.45e+04 7.31e+04 8.94e+04 7.80e+04 8.05e+04
## 4 3.87e+06 2.46e+06 2.79e+06 3.25e+06 1.79e+06 2.99e+06 3.31e+06
## 32 7.13e+05 3.55e+05 5.26e+05 5.70e+05 2.71e+05 5.22e+05 4.02e+05
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 9.82e+02 9.82e+02 2.24e+00 9.82e+02 3.38e+02 9.82e+02 1.65e+03
## 9 4.33e+04 1.14e+04 2.84e+04 4.33e+04 4.33e+04 4.33e+04 2.19e+04
## 210 1.90e+06 1.85e+06 1.13e+06 1.90e+06 1.29e+06 1.54e+06 1.06e+06
## 6 1.96e+04 1.53e+04 1.38e+04 1.34e+04 1.62e+04 1.25e+04 1.34e+04
## X2.10 X3.1 X3.2 X3.3 X3.4 X3.5 X3.6
## 1 2 1 1 1 1 1 2
## 2 2 3 3 3 3 3 3
## 3 0.25 0.5 0.5 0.5 0.5 0.5 0.5
## 7 4.61e+03 4.21e+03 2.38e+03 2.34e+03 3.53e+03 3.72e+03 3.87e+03
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 1.34e+07 1.21e+07 1.61e+07 1.15e+07 1.40e+07 1.48e+07 1.33e+07
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5 8.63e+04 6.84e+04 9.01e+04 9.01e+04 8.44e+04 9.42e+04 6.03e+04
## 4 2.81e+06 3.58e+06 3.31e+06 2.97e+06 2.25e+06 2.55e+06 2.70e+06
## 32 5.04e+05 2.55e+05 5.46e+05 4.27e+05 2.97e+05 4.33e+05 3.77e+05
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 1.65e+03 1.65e+03 1.35e+03 1.65e+03 1.65e+03 1.65e+03 1.65e+03
## 9 4.33e+04 2.36e+04 2.36e+04 2.36e+04 2.36e+04 2.36e+04 2.36e+04
## 210 1.61e+06 1.90e+06 1.90e+06 1.90e+06 1.63e+06 1.49e+06 1.90e+06
## 6 1.57e+04 9.02e+03 1.06e+04 1.65e+04 1.55e+04 1.35e+04 1.18e+04
## X3.7 X3.8 X3.9 X3.10 X4.1 X4.2 X4.3
## 1 2 2 2 2 1 1 1
## 2 3 3 3 3 4 4 4
## 3 0.5 0.5 0.5 0.5 1 1 1
## 7 3.28e+03 2.74e+03 3.39e+03 4.84e+03 2.65e+03 3.45e+03 2.67e+03
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 1.36e+07 9.84e+06 1.24e+07 1.38e+07 1.16e+07 1.79e+07 1.20e+07
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5 8.85e+04 8.19e+04 8.10e+04 8.98e+04 7.34e+04 9.21e+04 1.09e+05
## 4 1.78e+06 2.97e+06 2.89e+06 2.59e+06 2.24e+06 2.16e+06 2.36e+06
## 32 3.52e+05 4.96e+05 3.69e+05 4.55e+05 1.73e+05 2.99e+05 3.26e+05
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 1.65e+03 1.65e+03 1.22e+03 1.65e+03 5.71e+02 5.71e+02 5.71e+02
## 9 2.36e+04 2.36e+04 2.08e+04 2.64e+04 1.50e+04 1.50e+04 1.50e+04
## 210 1.66e+06 1.55e+06 7.76e+05 1.90e+06 1.36e+06 1.60e+06 1.34e+06
## 6 1.51e+04 1.56e+04 1.29e+04 1.54e+04 1.11e+04 1.33e+04 1.51e+04
## X4.4 X4.5 X4.6 X4.7 X4.8 X4.9 X4.10
## 1 1 1 2 2 2 2 2
## 2 4 4 4 4 4 4 4
## 3 1 1 1 1 1 1 1
## 7 3.28e+03 4.71e+03 3.01e+03 4.09e+03 3.07e+03 3.32e+03 2.67e+03
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 1.53e+07 1.77e+07 1.46e+07 1.33e+07 1.09e+07 1.27e+07 1.37e+07
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5 8.68e+04 8.13e+04 6.34e+04 6.70e+04 7.90e+04 8.11e+04 7.30e+04
## 4 1.84e+06 1.63e+06 1.77e+06 1.55e+06 3.02e+06 2.32e+06 1.76e+06
## 32 2.40e+05 2.15e+05 2.25e+05 2.21e+05 4.69e+05 2.79e+05 2.36e+05
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 5.71e+02 3.08e+02 5.71e+02 1.31e+02 5.71e+02 2.35e+02 1.61e+03
## 9 1.50e+04 1.50e+04 1.50e+04 1.50e+04 1.50e+04 1.50e+04 1.50e+04
## 210 8.82e+05 1.10e+06 1.48e+06 1.45e+06 1.48e+06 6.17e+05 1.33e+06
## 6 1.73e+04 1.19e+04 1.24e+04 1.16e+04 1.32e+04 1.35e+04 1.37e+04
## X5.1 X5.2 X5.3 X5.4 X5.5 X5.6 X5.7
## 1 1 1 1 1 1 2 2
## 2 5 5 5 5 5 5 5
## 3 2 2 2 2 2 2 2
## 7 3.63e+03 2.50e+03 1.76e+03 2.56e+03 2.81e+03 1.15e+03 2.93e+03
## 28 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 1.29e+07 1.59e+07 1.27e+07 1.57e+07 1.74e+07 9.80e+06 1.29e+07
## 29 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 30 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 5 6.51e+04 7.04e+04 8.74e+04 6.86e+04 7.87e+04 4.52e+04 7.71e+04
## 4 2.45e+06 2.03e+06 3.25e+06 2.19e+06 2.43e+06 2.04e+06 1.69e+06
## 32 2.36e+05 3.13e+05 5.74e+05 3.02e+05 3.98e+05 2.69e+05 2.42e+05
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 1.81e+02 5.87e+02 1.17e+03 1.74e+01 1.17e+03 1.17e+03 1.17e+03
## 9 1.11e+05 1.11e+05 1.11e+05 1.11e+05 1.11e+05 1.11e+05 1.11e+05
## 210 5.01e+05 4.58e+05 4.13e+05 3.37e+05 3.62e+05 2.88e+05 2.94e+05
## 6 9.34e+03 1.07e+04 1.52e+04 1.59e+04 1.23e+04 9.96e+03 1.38e+04
## X5.8 X5.9 X5.10
## 1 2 2 2
## 2 5 5 5
## 3 2 2 2
## 7 2.84e+03 2.27e+03 2.13e+03
## 28 <NA> <NA> <NA>
## 8 1.35e+07 1.16e+07 1.54e+07
## 29 <NA> <NA> <NA>
## 30 <NA> <NA> <NA>
## 5 7.77e+04 7.38e+04 7.11e+04
## 4 2.94e+06 1.96e+06 1.88e+06
## 32 5.11e+05 2.14e+05 3.20e+05
## 31 <NA> <NA> <NA>
## 110 1.17e+03 1.17e+03 1.65e+03
## 9 1.22e+05 1.11e+05 9.97e+04
## 210 6.43e+05 3.77e+05 3.37e+05
## 6 1.13e+04 1.19e+04 1.34e+04GetAbsoA function to get the absorbed drug constitutes by similarity analysis on the list of differential compounds and the list of drug constitutes:
GetAbso(drugData, A, simidata,sim = 80, filepath=getwd(),design = FALSE)## Name ID m.z RT.min. X0.1 X0.2
## 1 gender <NA> <NA> 1 1
## 2 group <NA> <NA> 0 0
## 3 timepoints(h) <NA> <NA> 0 0
## 7 octanoyl-rac-glycerol inx0001 219.1401 3.563800 4180 5080
## 16 liquiritin HMDB29520 417.1239 2.1398795 <NA> <NA>
## 17 formononetin HMDB05808 267.0631 3.1570558 <NA> <NA>
## 4 n-octadecanoic acid HMDB00827 283.2634 9.952400 3250000 2860000
## 32 myristic acid HMDB00806 227.2009 6.860767 578000 570000
## 6 phenylpyruvic acid HMDB00205 165.0545 3.521883 12600 13600
## X0.3 X0.4 X0.5 X0.6 X0.7 X0.8 X0.9 X0.10
## 1 1 1 1 2 2 2 2 2
## 2 0 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0 0
## 7 4770 4080 2.74e+03 4990 4430 4150 3540 3310
## 16 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 17 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 4 3110000 2160000 2.79e+06 3250000 1610000 2030000 2970000 2840000
## 32 425000 289000 4.08e+05 603000 168000 346000 442000 587000
## 6 20100 19100 1.93e+04 16300 19500 21000 17300 21900
## X1.1 X1.2 X1.3 X1.4 X1.5 X1.6 X1.7 X1.8
## 1 1 1 1 1 1 2 2 2
## 2 1 1 1 1 1 1 1 1
## 3 0.083 0.083 0.083 0.083 0.083 0.083 0.083 0.083
## 7 3.72e+03 1.62e+03 2.91e+03 4.73e+03 3.78e+03 1.90e+03 2.83e+03 2.99e+03
## 16 6.15e-01 6.15e-01 6.18e-01 8.72e-01 6.15e-01 6.15e-01 6.15e-01 6.15e-01
## 17 1.50e+01 2.93e+00 5.09e+00 1.33e+00 1.38e+00 5.77e+00 2.29e+00 3.72e+00
## 4 4.40e+06 4.36e+06 4.23e+06 2.24e+06 2.42e+06 2.65e+06 1.81e+06 2.30e+06
## 32 3.78e+05 7.13e+05 7.07e+05 3.12e+05 4.87e+05 4.55e+05 3.13e+05 5.13e+05
## 6 1.04e+04 1.42e+04 1.96e+04 1.79e+04 1.35e+04 1.41e+04 1.49e+04 1.62e+04
## X1.9 X1.10 X2.1 X2.2 X2.3 X2.4 X2.5 X2.6
## 1 2 2 1 1 1 1 1 2
## 2 1 1 2 2 2 2 2 2
## 3 0.083 0.083 0.25 0.25 0.25 0.25 0.25 0.25
## 7 2.83e+03 4.35e+03 3.03e+03 3.86e+03 3.88e+03 4.29e+03 2.72e+03 4.11e+03
## 16 3.56e-01 6.15e-01 2.15e-01 1.23e+00 5.04e-01 9.23e-01 7.42e-01 9.23e-01
## 17 3.68e+00 1.69e+00 4.14e+01 2.35e+01 3.63e+01 2.38e+01 3.35e+01 4.12e+01
## 4 3.26e+06 2.92e+06 4.40e+06 4.39e+06 3.87e+06 2.46e+06 2.79e+06 3.25e+06
## 32 4.74e+05 4.23e+05 3.98e+05 7.13e+05 7.13e+05 3.55e+05 5.26e+05 5.70e+05
## 6 1.10e+04 1.64e+04 1.29e+04 1.43e+04 1.96e+04 1.53e+04 1.38e+04 1.34e+04
## X2.7 X2.8 X2.9 X2.10 X3.1 X3.2 X3.3 X3.4
## 1 2 2 2 2 1 1 1 1
## 2 2 2 2 2 3 3 3 3
## 3 0.25 0.25 0.25 0.25 0.5 0.5 0.5 0.5
## 7 4.40e+03 2.93e+03 4.93e+03 4.61e+03 4.21e+03 2.38e+03 2.34e+03 3.53e+03
## 16 1.29e+00 1.29e+00 7.61e-01 1.35e+00 2.71e+00 1.71e+00 2.71e+00 2.71e+00
## 17 1.78e+01 1.99e+01 6.45e+00 1.93e+01 7.15e+01 4.83e+01 4.07e+01 3.35e+01
## 4 1.79e+06 2.99e+06 3.31e+06 2.81e+06 3.58e+06 3.31e+06 2.97e+06 2.25e+06
## 32 2.71e+05 5.22e+05 4.02e+05 5.04e+05 2.55e+05 5.46e+05 4.27e+05 2.97e+05
## 6 1.62e+04 1.25e+04 1.34e+04 1.57e+04 9.02e+03 1.06e+04 1.65e+04 1.55e+04
## X3.5 X3.6 X3.7 X3.8 X3.9 X3.10 X4.1 X4.2
## 1 1 2 2 2 2 2 1 1
## 2 3 3 3 3 3 3 4 4
## 3 0.5 0.5 0.5 0.5 0.5 0.5 1 1
## 7 3.72e+03 3.87e+03 3.28e+03 2.74e+03 3.39e+03 4.84e+03 2.65e+03 3.45e+03
## 16 2.71e+00 2.71e+00 8.45e-01 2.71e+00 2.71e+00 2.61e+00 2.71e+00 1.68e+00
## 17 4.56e+01 6.56e+01 7.15e+01 5.41e+01 5.40e+01 5.01e+01 1.47e+01 1.38e+01
## 4 2.55e+06 2.70e+06 1.78e+06 2.97e+06 2.89e+06 2.59e+06 2.24e+06 2.16e+06
## 32 4.33e+05 3.77e+05 3.52e+05 4.96e+05 3.69e+05 4.55e+05 1.73e+05 2.99e+05
## 6 1.35e+04 1.18e+04 1.51e+04 1.56e+04 1.29e+04 1.54e+04 1.11e+04 1.33e+04
## X4.3 X4.4 X4.5 X4.6 X4.7 X4.8 X4.9 X4.10
## 1 1 1 1 2 2 2 2 2
## 2 4 4 4 4 4 4 4 4
## 3 1 1 1 1 1 1 1 1
## 7 2.67e+03 3.28e+03 4.71e+03 3.01e+03 4.09e+03 3.07e+03 3.32e+03 2.67e+03
## 16 2.71e+00 2.71e+00 2.71e+00 2.71e+00 2.71e+00 2.71e+00 2.01e+00 2.71e+00
## 17 1.37e+01 1.49e+01 8.77e+00 6.58e+00 3.45e+01 3.24e+01 1.20e+01 1.86e+01
## 4 2.36e+06 1.84e+06 1.63e+06 1.77e+06 1.55e+06 3.02e+06 2.32e+06 1.76e+06
## 32 3.26e+05 2.40e+05 2.15e+05 2.25e+05 2.21e+05 4.69e+05 2.79e+05 2.36e+05
## 6 1.51e+04 1.73e+04 1.19e+04 1.24e+04 1.16e+04 1.32e+04 1.35e+04 1.37e+04
## X5.1 X5.2 X5.3 X5.4 X5.5 X5.6 X5.7 X5.8
## 1 1 1 1 1 1 2 2 2
## 2 5 5 5 5 5 5 5 5
## 3 2 2 2 2 2 2 2 2
## 7 3.63e+03 2.50e+03 1.76e+03 2.56e+03 2.81e+03 1.15e+03 2.93e+03 2.84e+03
## 16 2.71e+00 2.21e+00 2.71e+00 2.71e+00 2.71e+00 2.71e+00 2.71e+00 9.90e-01
## 17 1.57e+00 1.12e+00 5.93e+00 4.70e-01 2.25e+00 2.42e+00 3.24e+00 5.81e+00
## 4 2.45e+06 2.03e+06 3.25e+06 2.19e+06 2.43e+06 2.04e+06 1.69e+06 2.94e+06
## 32 2.36e+05 3.13e+05 5.74e+05 3.02e+05 3.98e+05 2.69e+05 2.42e+05 5.11e+05
## 6 9.34e+03 1.07e+04 1.52e+04 1.59e+04 1.23e+04 9.96e+03 1.38e+04 1.13e+04
## X5.9 X5.10
## 1 2 2
## 2 5 5
## 3 2 2
## 7 2.27e+03 2.13e+03
## 16 2.71e+00 2.71e+00
## 17 4.47e+00 3.27e+00
## 4 1.96e+06 1.88e+06
## 32 2.14e+05 3.20e+05
## 6 1.19e+04 1.34e+04GetSecdAbsoA function to get secondary metabolites of the absorbed drug constitutes:
GetSecdAbso(A,B,C,simidata,sim=80,filepath=getwd(),design=FALSE)## Name ID m.z RT.min. X0.1
## 1 gender <NA> <NA> 1
## 2 group <NA> <NA> 0
## 3 timepoints(h) <NA> <NA> 0
## 10 formononetin glucuronide HMDB41735 445.1206 10.2335500 <NA>
## 11 gancaonin V HMDB37586 311.1301 2.2231667 <NA>
## 12 isoquercitrin HMDB37362 463.0988 2.0986452 <NA>
## 13 ceanothic acid HMDB36851 485.3250 3.4732833 <NA>
## 14 ganoderic acid H HMDB35987 571.2883 3.5425833 <NA>
## 15 isoformononetin HMDB33994 269.0809 2.4982167 <NA>
## 8 1,2,3-propanetricarboxylic acid HMDB31193 73.0000 15.657182 11000000
## 5 tryptophan HMDB00929 203.0819 1.352400 76200
## 18 trigonelline HMDB00875 136.0404 2.5085333 <NA>
## 19 histamine HMDB00870 112.0763 0.7084167 <NA>
## 20 phytanic acid HMDB00801 311.2948 10.8229833 <NA>
## 31 hyodeoxycholic acid HMDB00733 391.2842 3.574000 33500
## 110 glycolithocholic acid HMDB00698 432.3107 3.420900 971
## 21 cholesterol sulfate HMDB00653 465.3041 6.6551167 <NA>
## 22 cytosine HMDB00630 110.0349 9.7993333 <NA>
## 23 erythronic acid HMDB00613 135.0293 0.5236500 <NA>
## 24 chenodeoxycholic acid HMDB00518 391.2845 3.9222000 <NA>
## 25 2-aminobutyric acid HMDB00452 104.0545 0.7084167 <NA>
## 26 2-pyrocatechuic acid HMDB00397 153.0187 2.4666167 <NA>
## 27 urea HMDB00294 100.0000 7.1697798 <NA>
## X0.2 X0.3 X0.4 X0.5 X0.6 X0.7 X0.8
## 1 1 1 1 1 2 2 2
## 2 0 0 0 0 0 0 0
## 3 0 0 0 0 0 0 0
## 10 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 11 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 12 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 13 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 14 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 15 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 8 10100000 10900000 14500000 1.38e+07 13200000 11800000 12300000
## 5 101000 125000 96100 1.18e+05 87900 101000 115000
## 18 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 19 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 20 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 31 9930 22200 13300 2.57e+04 7800 24600 33500
## 110 971 971 971 5.09e+00 971 971 971
## 21 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 22 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 23 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 24 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 25 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 26 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 27 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## X0.9 X0.10 X1.1 X1.2 X1.3 X1.4 X1.5
## 1 2 2 1 1 1 1 1
## 2 0 0 1 1 1 1 1
## 3 0 0 0.083 0.083 0.083 0.083 0.083
## 10 <NA> <NA> 8.55e+02 7.07e+02 8.55e+02 1.76e+02 3.57e+02
## 11 <NA> <NA> 8.76e+04 8.54e+03 3.52e+04 3.11e+04 2.95e+04
## 12 <NA> <NA> 2.17e+03 2.68e+03 2.28e+03 2.71e+03 2.25e+03
## 13 <NA> <NA> 3.12e+00 1.47e+02 1.77e+02 1.77e+02 1.47e+02
## 14 <NA> <NA> 3.27e+06 4.61e+06 2.24e+06 3.41e+06 2.83e+06
## 15 <NA> <NA> 3.90e+02 7.76e+02 1.60e+02 1.37e+02 2.29e+02
## 8 10400000 13400000 1.25e+07 1.63e+07 9.99e+06 1.54e+07 1.82e+07
## 5 106000 105000 7.24e+04 9.80e+04 1.14e+05 9.10e+04 9.62e+04
## 18 <NA> <NA> 9.69e+02 1.03e+03 1.41e+03 1.31e+03 1.76e+03
## 19 <NA> <NA> 4.82e-01 1.98e+02 1.10e+02 1.88e+01 1.10e+02
## 20 <NA> <NA> 3.92e+04 3.92e+04 2.50e+04 5.45e+03 2.11e+04
## 31 20500 8550 <NA> <NA> <NA> <NA> <NA>
## 110 971 971 3.10e+01 4.79e+00 2.82e+02 2.82e+02 2.82e+02
## 21 <NA> <NA> 1.30e+05 1.75e+05 1.61e+05 1.46e+05 8.07e+04
## 22 <NA> <NA> 4.63e+04 4.45e+04 4.23e+04 3.75e+04 3.98e+04
## 23 <NA> <NA> 2.03e+02 7.88e+02 2.11e+03 1.58e+03 1.31e+03
## 24 <NA> <NA> 9.69e+02 1.03e+03 1.41e+03 1.31e+03 1.76e+03
## 25 <NA> <NA> 4.82e-01 1.98e+02 1.10e+02 1.88e+01 1.10e+02
## 26 <NA> <NA> 3.92e+04 3.92e+04 2.50e+04 5.45e+03 2.11e+04
## 27 <NA> <NA> 8.89e+02 4.24e+02 5.17e+02 8.45e+02 5.30e+02
## X1.6 X1.7 X1.8 X1.9 X1.10 X2.1 X2.2
## 1 2 2 2 2 2 1 1
## 2 1 1 1 1 1 2 2
## 3 0.083 0.083 0.083 0.083 0.083 0.25 0.25
## 10 8.55e+02 8.76e+02 8.55e+02 2.16e+03 8.55e+02 6.99e+02 2.00e+03
## 11 3.76e+03 1.88e+04 4.66e+04 7.72e+04 1.13e+04 8.88e+04 7.52e+03
## 12 2.25e+03 2.03e+03 1.91e+03 1.98e+03 2.13e+03 1.32e+03 2.19e+03
## 13 8.88e+01 1.47e+02 1.47e+02 1.47e+02 7.38e+01 1.34e+02 1.34e+02
## 14 3.59e+06 3.20e+06 1.91e+06 3.86e+06 3.21e+06 8.83e+05 1.04e+06
## 15 5.76e+01 3.28e+02 2.64e+02 3.08e+01 2.64e+02 2.79e+02 5.40e+02
## 8 1.27e+07 1.24e+07 1.13e+07 1.30e+07 1.36e+07 1.16e+07 1.95e+07
## 5 6.97e+04 8.07e+04 8.15e+04 8.88e+04 8.16e+04 9.26e+04 1.05e+05
## 18 1.07e+03 5.85e+02 1.24e+03 1.23e+03 9.00e+02 9.47e+02 1.75e+03
## 19 1.98e+02 2.68e+01 1.10e+02 1.40e+02 1.90e+02 2.07e+02 2.55e+02
## 20 1.27e+04 5.83e+03 1.35e+04 9.84e+03 1.29e+04 3.92e+04 3.92e+04
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 2.82e+02 1.23e+02 2.82e+02 6.10e+02 6.41e+02 1.68e+01 6.44e+02
## 21 5.02e+04 4.89e+04 7.98e+04 7.27e+04 1.16e+05 1.99e+05 2.39e+05
## 22 4.22e+04 3.91e+04 3.72e+04 4.47e+04 4.47e+04 4.41e+04 4.84e+04
## 23 2.50e+03 8.93e+02 1.20e+03 1.40e+03 1.14e+03 2.23e+02 5.55e+02
## 24 1.07e+03 5.85e+02 1.24e+03 1.23e+03 9.00e+02 9.47e+02 1.75e+03
## 25 1.98e+02 2.68e+01 1.10e+02 1.40e+02 1.90e+02 2.06e+03 1.26e+03
## 26 1.27e+04 5.83e+03 1.35e+04 9.84e+03 1.29e+04 3.92e+04 3.92e+04
## 27 7.57e+02 3.74e+02 6.74e+02 5.25e+01 1.04e+02 8.30e+01 6.13e+02
## X2.3 X2.4 X2.5 X2.6 X2.7 X2.8 X2.9
## 1 1 1 1 2 2 2 2
## 2 2 2 2 2 2 2 2
## 3 0.25 0.25 0.25 0.25 0.25 0.25 0.25
## 10 6.56e+02 3.11e+03 3.11e+03 2.27e+03 2.27e+03 3.42e+02 4.51e+02
## 11 4.43e+04 3.00e+04 2.25e+04 6.20e+02 1.66e+04 3.93e+04 1.71e+04
## 12 2.43e+03 1.79e+03 1.96e+03 1.87e+03 1.26e+03 1.68e+03 1.57e+03
## 13 1.77e+02 1.51e+02 7.83e+01 1.34e+02 1.25e+02 1.34e+02 4.22e+00
## 14 2.65e+06 1.06e+06 9.35e+05 1.05e+06 1.10e+06 9.60e+05 1.20e+06
## 15 8.10e+02 8.50e+02 3.78e+02 8.50e+02 8.50e+02 4.03e+02 1.98e+02
## 8 1.48e+07 1.73e+07 1.63e+07 1.45e+07 1.57e+07 9.90e+06 1.43e+07
## 5 1.14e+05 8.09e+04 9.45e+04 7.31e+04 8.94e+04 7.80e+04 8.05e+04
## 18 9.51e+02 4.83e+02 1.40e+03 9.44e+02 1.21e+03 1.20e+03 1.04e+03
## 19 2.95e+00 2.07e+02 2.55e+02 1.39e+01 2.07e+02 2.07e+02 2.55e+02
## 20 2.86e+04 8.93e+03 2.26e+04 1.86e+04 1.12e+04 1.33e+04 1.30e+04
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 9.82e+02 9.82e+02 2.24e+00 9.82e+02 3.38e+02 9.82e+02 1.65e+03
## 21 1.71e+05 1.82e+05 1.04e+05 8.03e+04 7.16e+04 9.96e+04 8.52e+04
## 22 4.36e+04 4.83e+04 4.88e+04 4.33e+04 4.51e+04 4.29e+04 4.90e+04
## 23 3.28e+02 1.21e+03 1.55e+02 1.83e+03 9.80e+02 1.29e+03 9.43e+02
## 24 9.51e+02 4.83e+02 1.40e+03 9.44e+02 1.21e+03 1.20e+03 1.04e+03
## 25 2.11e+03 2.21e+03 9.55e+02 1.01e+03 2.06e+03 2.21e+03 1.26e+03
## 26 2.86e+04 8.93e+03 2.26e+04 1.86e+04 1.12e+04 1.33e+04 1.30e+04
## 27 4.09e+02 5.89e+02 8.22e+02 5.74e+02 2.11e+02 7.36e+02 7.08e+01
## X2.10 X3.1 X3.2 X3.3 X3.4 X3.5 X3.6
## 1 2 1 1 1 1 1 2
## 2 2 3 3 3 3 3 3
## 3 0.25 0.5 0.5 0.5 0.5 0.5 0.5
## 10 6.14e+02 1.25e+03 6.10e+02 1.25e+03 2.40e+03 5.77e+02 1.25e+03
## 11 2.22e+03 9.09e+04 9.58e+03 1.69e+04 8.23e+03 1.89e+04 2.43e+03
## 12 2.08e+03 1.78e+03 7.96e+02 1.52e+03 1.81e+03 1.60e+03 1.67e+03
## 13 1.34e+02 1.29e+02 1.25e+02 1.58e+02 1.29e+02 6.32e+01 1.77e+02
## 14 9.61e+05 7.42e+05 1.24e+06 1.71e+06 7.56e+05 5.44e+05 7.59e+05
## 15 3.98e+02 8.50e+02 8.50e+02 8.50e+02 8.50e+02 8.47e+02 8.50e+02
## 8 1.34e+07 1.21e+07 1.61e+07 1.15e+07 1.40e+07 1.48e+07 1.33e+07
## 5 8.63e+04 6.84e+04 9.01e+04 9.01e+04 8.44e+04 9.42e+04 6.03e+04
## 18 1.23e+03 1.05e+03 1.16e+03 6.99e+02 8.31e+02 1.65e+03 4.19e+02
## 19 2.55e+02 7.86e+01 1.24e+02 1.85e+02 1.40e+02 2.55e+02 2.24e+02
## 20 1.43e+04 3.92e+04 3.23e+04 2.43e+04 7.69e+03 2.01e+04 1.40e+04
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 1.65e+03 1.65e+03 1.35e+03 1.65e+03 1.65e+03 1.65e+03 1.65e+03
## 21 1.27e+05 1.36e+05 1.51e+05 1.41e+05 1.29e+05 9.40e+04 5.56e+04
## 22 4.12e+04 4.73e+04 4.97e+04 5.04e+04 5.19e+04 5.25e+04 5.23e+04
## 23 8.89e+02 9.24e+02 1.35e+03 2.44e+03 1.77e+03 3.63e+02 2.26e+03
## 24 1.23e+03 7.42e+05 1.24e+06 1.71e+06 7.56e+05 5.44e+05 7.59e+05
## 25 2.16e+03 2.35e+04 2.36e+04 3.02e+04 1.74e+04 4.46e+04 1.87e+04
## 26 1.43e+04 1.36e+05 1.76e+05 2.18e+05 1.97e+05 1.80e+05 1.74e+05
## 27 8.26e+02 2.37e+04 2.26e+04 3.33e+04 3.56e+04 2.79e+04 2.60e+04
## X3.7 X3.8 X3.9 X3.10 X4.1 X4.2 X4.3
## 1 2 2 2 2 1 1 1
## 2 3 3 3 3 4 4 4
## 3 0.5 0.5 0.5 0.5 1 1 1
## 10 1.25e+03 1.41e+03 1.00e+03 1.50e+03 1.68e+03 4.62e+02 1.68e+03
## 11 4.50e+03 9.09e+04 1.05e+03 3.03e+03 9.09e+04 3.89e+03 3.10e+04
## 12 1.02e+03 1.42e+03 1.09e+03 2.14e+03 1.42e+03 1.80e+03 1.86e+03
## 13 1.29e+02 5.13e+01 1.29e+02 1.37e+02 1.52e+02 1.42e+02 1.77e+02
## 14 5.60e+05 6.65e+05 1.11e+06 2.41e+06 5.57e+06 4.81e+06 5.57e+06
## 15 5.63e+02 8.50e+02 8.50e+02 8.50e+02 8.50e+02 8.50e+02 6.41e+02
## 8 1.36e+07 9.84e+06 1.24e+07 1.38e+07 1.16e+07 1.79e+07 1.20e+07
## 5 8.85e+04 8.19e+04 8.10e+04 8.98e+04 7.34e+04 9.21e+04 1.09e+05
## 18 1.19e+03 1.48e+03 1.67e+03 1.02e+03 1.10e+03 1.53e+03 1.09e+03
## 19 6.33e+01 1.85e+02 4.30e+00 1.85e+02 1.33e+02 2.55e+02 1.50e+02
## 20 8.20e+03 1.64e+04 1.67e+04 1.06e+04 2.55e+04 2.44e+04 1.66e+04
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 1.65e+03 1.65e+03 1.22e+03 1.65e+03 5.71e+02 5.71e+02 5.71e+02
## 21 6.85e+04 1.04e+05 6.49e+04 9.88e+04 2.20e+05 2.02e+05 1.86e+05
## 22 4.19e+04 4.63e+04 4.95e+04 4.33e+04 4.42e+04 5.08e+04 5.08e+04
## 23 2.60e+03 1.26e+03 1.44e+03 2.16e+03 6.14e+02 2.22e+03 2.91e+03
## 24 5.60e+05 6.65e+05 1.11e+06 2.41e+06 2.41e+06 2.41e+06 2.41e+06
## 25 1.73e+04 2.82e+04 2.30e+04 2.49e+04 2.32e+04 2.28e+04 2.79e+04
## 26 1.99e+05 1.91e+05 1.73e+05 2.05e+05 1.25e+05 2.01e+05 1.94e+05
## 27 3.26e+04 3.49e+04 2.72e+04 3.33e+04 3.19e+04 2.95e+04 3.76e+04
## X4.4 X4.5 X4.6 X4.7 X4.8 X4.9 X4.10
## 1 1 1 2 2 2 2 2
## 2 4 4 4 4 4 4 4
## 3 1 1 1 1 1 1 1
## 10 6.14e+02 6.40e+02 7.11e+02 3.11e+03 5.53e+02 1.68e+03 4.50e+02
## 11 1.45e+04 5.12e+04 4.70e+04 1.08e+04 7.74e+04 4.09e+04 3.06e+04
## 12 1.61e+03 1.70e+03 1.89e+03 1.54e+03 9.78e+02 8.86e+02 1.27e+03
## 13 1.08e+02 6.62e+01 1.42e+02 4.03e+01 1.42e+02 1.52e+02 1.42e+02
## 14 4.76e+06 2.11e+06 1.09e+06 1.78e+06 2.18e+06 4.74e+06 1.06e+06
## 15 8.50e+02 7.45e+02 6.70e+02 8.50e+02 8.50e+02 8.50e+02 8.50e+02
## 8 1.53e+07 1.77e+07 1.46e+07 1.33e+07 1.09e+07 1.27e+07 1.37e+07
## 5 8.68e+04 8.13e+04 6.34e+04 6.70e+04 7.90e+04 8.11e+04 7.30e+04
## 18 1.47e+03 8.11e+02 8.69e+02 1.51e+03 1.29e+03 1.28e+03 1.25e+03
## 19 1.50e+02 1.09e+02 2.55e+02 1.40e+02 2.15e+01 8.68e+01 1.82e+02
## 20 8.79e+03 1.13e+04 3.64e+03 1.01e+04 1.77e+04 9.52e+03 1.06e+04
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 5.71e+02 3.08e+02 5.71e+02 1.31e+02 5.71e+02 2.35e+02 1.61e+03
## 21 1.89e+05 9.95e+04 7.83e+04 6.57e+04 1.11e+05 7.89e+04 1.19e+05
## 22 4.80e+04 5.19e+04 4.90e+04 4.39e+04 4.44e+04 5.17e+04 4.72e+04
## 23 2.91e+03 1.58e+02 2.91e+03 1.71e+03 1.43e+03 2.04e+03 8.41e+02
## 24 1.17e+06 1.23e+06 1.01e+06 1.04e+06 2.24e+06 2.41e+06 2.41e+06
## 25 2.21e+04 4.15e+04 1.71e+04 1.54e+04 2.80e+04 2.60e+04 2.16e+04
## 26 1.85e+05 1.77e+05 1.73e+05 1.88e+05 1.78e+05 1.66e+05 1.98e+05
## 27 3.46e+04 2.64e+04 3.16e+04 3.71e+04 3.67e+04 3.63e+04 4.31e+04
## X5.1 X5.2 X5.3 X5.4 X5.5 X5.6 X5.7
## 1 1 1 1 1 1 2 2
## 2 5 5 5 5 5 5 5
## 3 2 2 2 2 2 2 2
## 10 3.77e+02 4.21e+02 1.58e+03 3.11e+03 2.48e+03 1.44e+03 2.48e+03
## 11 1.44e+03 1.65e+03 1.85e+03 1.14e+03 1.45e+03 1.22e+03 1.45e+03
## 12 1.13e+02 1.62e+02 1.08e+02 1.69e+02 2.70e+01 2.48e+01 3.22e+01
## 13 7.50e+01 9.20e+01 1.23e+02 7.60e+01 1.77e+02 8.80e+01 1.77e+02
## 14 1.69e+04 1.21e+04 1.54e+04 1.51e+04 2.83e+04 1.10e+04 1.74e+04
## 15 4.09e+02 3.75e+02 9.18e+01 4.09e+02 9.30e+01 1.81e+02 4.09e+02
## 8 1.29e+07 1.59e+07 1.27e+07 1.57e+07 1.74e+07 9.80e+06 1.29e+07
## 5 6.51e+04 7.04e+04 8.74e+04 6.86e+04 7.87e+04 4.52e+04 7.71e+04
## 18 1.09e+03 1.12e+03 1.43e+03 1.61e+03 7.71e+02 8.01e+02 1.47e+03
## 19 1.15e+02 7.61e+00 8.39e-01 1.02e+02 5.27e+01 1.16e+02 9.80e+01
## 20 2.37e+04 1.45e+04 1.72e+04 1.06e+04 1.91e+04 9.62e+03 1.26e+04
## 31 <NA> <NA> <NA> <NA> <NA> <NA> <NA>
## 110 1.81e+02 5.87e+02 1.17e+03 1.74e+01 1.17e+03 1.17e+03 1.17e+03
## 21 2.02e+05 1.90e+05 1.85e+05 1.94e+05 1.16e+05 5.55e+04 7.96e+04
## 22 4.42e+04 5.17e+04 5.17e+04 5.13e+04 5.24e+04 5.26e+04 4.30e+04
## 23 5.17e+02 1.66e+03 1.59e+03 1.74e+03 3.37e+02 3.03e+02 2.03e+03
## 24 7.07e+04 3.32e+04 2.41e+04 1.45e+04 2.59e+04 1.46e+03 5.03e+04
## 25 1.44e+03 1.65e+03 1.85e+03 1.14e+03 1.45e+03 1.22e+03 1.45e+03
## 26 1.13e+02 1.62e+02 1.08e+02 1.69e+02 2.70e+01 2.48e+01 3.22e+01
## 27 4.31e+04 4.31e+04 4.31e+04 4.31e+04 4.31e+04 4.31e+04 4.31e+04
## X5.8 X5.9 X5.10
## 1 2 2 2
## 2 5 5 5
## 3 2 2 2
## 10 1.47e+03 5.91e+02 2.48e+03
## 11 9.35e+02 9.08e+02 1.19e+03
## 12 2.38e+02 1.36e+02 1.13e+02
## 13 9.70e+01 9.90e+01 1.02e+02
## 14 4.33e+04 1.58e+04 1.58e+04
## 15 8.50e+02 1.88e+02 8.50e+02
## 8 1.35e+07 1.16e+07 1.54e+07
## 5 7.77e+04 7.38e+04 7.11e+04
## 18 1.18e+03 9.28e+02 1.02e+03
## 19 7.31e+01 7.31e+01 9.24e+01
## 20 1.66e+04 8.01e+03 8.55e+03
## 31 <NA> <NA> <NA>
## 110 1.17e+03 1.17e+03 1.65e+03
## 21 1.10e+05 7.94e+04 1.13e+05
## 22 4.83e+04 5.08e+04 4.68e+04
## 23 1.44e+03 1.62e+03 8.24e+02
## 24 1.03e+05 6.59e+03 2.69e+04
## 25 9.35e+02 9.08e+02 1.19e+03
## 26 2.38e+02 1.36e+02 1.13e+02
## 27 4.31e+04 4.31e+04 4.31e+04PKsA function to calculate the 7 pharmacokinetics parameters (Tmax, Cmax, AUC, CL, Tlast, Tfirst, Cmin) and plot the time-intensity curves for specified compounds.
A list of metabolites and 7 pharmacokinetics parameters (Tmax,Cmax,AUC,CL,Tlast,Tfirst,Cmin) of specified compound:
data("C")
data("design")
pks<-PKs(C,d.point="mean",d.ebar="SE",filepath=getwd(),design=FALSE)
knitr::kable(pks[c(1:10),],align = 'c')| Name | ID | m.z | R.T.min. | Tmax | Tlast | Tfirst | Cmax | Cmin | AUC | CL | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 7 | octanoyl-rac-glycerol | inx0001 | 219.1401 | 3.563800 | 0.00 | 2 | 0 | 4.127e+03 | 2458 | 6.359417e+03 | 0 |
| 16 | liquiritin | HMDB29520 | 417.1239 | 2.1398795 | 1.00 | 2 | 0 | 2.537e+00 | 0 | 4.321104e+00 | NA |
| 17 | formononetin | HMDB05808 | 267.0631 | 3.1570558 | 0.50 | 2 | 0 | 5.349e+01 | 0 | 4.035518e+01 | NA |
| 4 | n-octadecanoic acid | HMDB00827 | 283.2634 | 9.952400 | 0.25 | 2 | 0 | 3.206e+06 | 2065000 | 4.888712e+06 | 0 |
| 6 | phenylpyruvic acid | HMDB00205 | 165.0545 | 3.521883 | 0.00 | 2 | 0 | 1.807e+04 | 12380 | 2.693894e+04 | 0 |
| NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| NA.1 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| NA.2 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| NA.3 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| NA.4 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
The time-intensity curves for specified compounds are in the folder named “PKs” which is created automatically.
CorrPlotA function to calculate the correlation coefficients and plot the correlation diagram (8 types) of two input datasets.
data("B")
data("C")
CorrPlot(dataset1=B,dataset2=C,cor.method="pearson",filepath=getwd(),fig.form="heatmap",design = FALSE)ScatPlotA function to plot the PCA or PLSDA score figures and trajectories on input data:
data("A")
ScatPlot(scat.data=A,scform="PCA",num.of.cp=2,filepath=getwd(),design=FALSE)HeatMapA function to plot the heatmap and clusters of input data:
data("A")
HeatMap(data=A,cluster="both",scale="row",filepath=getwd(),design=FALSE)help(package = 'polyPK', help_type = 'html')
# or see a standalone list of vignettes
browseVignettes('polyPK')