AAmass |
Molecular mass for amino-acids |
AucROC |
AUC from ROC-curves |
cleanListCoNames |
Selective batch cleaning of sample- (ie column-) names in list |
combineMultFilterNAimput |
Combine multiple filters on NA-imputed data |
convAASeq2mass |
Molecular mass for amino-acids |
corColumnOrder |
Order columns in list of matrixes (or matrix) |
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). |
extractTestingResults |
Extract results from moderated t-tests |
extrSpeciesAnnot |
Extract species annotation |
foldChangeArrow2 |
Add arrow for expected Fold-Change to VolcanoPlot or MA-plot |
isolNAneighb |
Isolate NA-neighbours |
massDeFormula |
molecular mass from chemical formula |
matrixNAinspect |
Histogram of content of NAs in matrix |
matrixNAneighbourImpute |
Imputation of NA-values based on non-NA replicates |
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 uniqueIdentifier, entryName, proteinName, GN) in separate columns. |
readMassChroQFile |
Read tabulated files imported from MassChroQ |
readMaxQuantFile |
Read proteinGroups.txt files exported from MaxQuant |
readOpenMSFile |
Read csv files exported by OpenMS |
readProlineFile |
Read csv or txt files exported from Proline and MS-Angel |
readProtDiscovFile |
Read tabulated files exported by ProteomeDiscoverer |
readSdrf |
Read proteomics meta-data as sdrf file This function allows reading proteomics meta-data from sdrf file, as they are provided on https://github.com/bigbio/proteomics-metadata-standard. Then, a data.frame with all annotation data will be returned. To stay conform with the (non-obligatory) recommendations, column-names will be shown as lower caps. The package utils must be installed. |
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' ! |
replMissingProtNames |
Complement missing EntryNames in annotation |
summarizeForROC |
Summarize statistical test result for plotting ROC-curves |
test2grp |
t-test each line of 2 groups of data |
testRobustToNAimputation |
Pair-wise testing robust to NA-imputation |
VolcanoPlotW2 |
Volcano-plot (Statistical Test Outcome versus Relative Change) |
writeFasta2 |
Write sequences in fasta format to file This function writes sequences from character vector as fasta formatted file (from UniProt) Line-headers are based on names of elements of input vector 'prot'. This function also allows comparing the main vector of sequences with a reference vector 'ref' to check if any of the sequences therein are truncated. |