Proteomics Data Analysis Functions

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Documentation for package ‘wrProteo’ version 1.0.0

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combineMultFilterNAimput Combine multiple filters on NA-imputed data
countNoOfCommonPeptides Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides Compare in-silico digested proteomes for unique and shared peptides, counts per protein or as peptides. The in-silico digestion may be performed separately using the package cleaver. Note: input must be list (or multiple names lists) of proteins with their respective peptides (eg by in-silico digestion).
extrSpeciesAnnot Extract species annotation
matrixNAinspect Histogram of content of NAs in matrix
matrixNAneighbourImpute Impute random values to NAs in matrix based on replicates (neighbour) values
plotROC Plot ROC curves
razorNoFilter Filter based on either number of total peptides and specific peptides or number of razor petides
readFasta2 Read file of protein sequences in fasta format Read fasta formatted file (from Uniprot) to extract (protein) sequences and name. If 'tableOut=TRUE' output may be organized as matrix for separating meta-annotationExtract, see also FASTA-headers.
readProlineFile Read csv or txt files exported from MS-Angel and Proline
removeSampleInList Remove samples/columns from list of matrixes Remove samples (ie columns) from every instance of list of matrixes. Note: This function assumes same order of columns in list-elements 'listElem' !
summarizeForROC Summarize statistical test result for plotting ROC-curves
test2grp t-test each line of 2 groups of data
testRobustToNAimputation Test robust to NA-imputation