AAmass |
Molecular mass for amino-acids |
combineMultFilterNAimput |
Combine multiple filters on NA-imputed data |
convAASeq2mass |
Molecular mass for amino-acids |
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 |
massDeFormula |
molecular mass from chemical formula |
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-annotation (eg GeneName, OrganismName, ProteinName) in separate columns. |
readMaxQuantFile |
Read csv or txt files exported from MS-Angel and Proline |
readPDExport |
Read tabulated files imported from Thermo ProteomeDiscoverer |
readProlineFile |
Read csv or txt files exported from MS-Angel and Proline |
readUCSCtable |
Read annotation files from UCSC |
readUniProtExport |
Read protein annotation as exported from UniProt batch-conversion |
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 |