Man pages for kroganlab/artMS
Analytical R tools for Mass Spectrometry

avg_intensity_RTSummarize average intensity and retention time per protein
castMaxQToWideLong to Wide format using the 'Sequence' column of the...
castMaxQToWidePTMLong to Wide format selecting the 'Modified.sequence' column...
changeColumnNameChange a specific column name in a given data.frame
checkIfFileCheck if an input is a file or a data object
filterDataFiltering data
filterMaxqDataRemove contaminants and empty proteins
filterNumUniqPepFilter MaxQuant data based on Number of Unique Peptides
getMSstatsFormatGenerate MSstats format object and file
interaction_overlapLook for Overlap between Two Groups
isEvidenceNewVersionCheck if a given evidencee file was generated by a new...
mainMain Function
MaxQToSaintConvert MaxQuant file into a format to work with SAINT
mergeMaxQDataWithKeysMerge evidence and keys files
mq2mssConvert MaxQuant evidence file to MSStats compatible format
mq2mss_PTMMaxQuant PTM to MSStats.
MQutil.annotateAnnotate MSStats results file.
MQutil.concatConcatenate MaxQuant search result files
MQutil.mapSitesBackMap the results back into sites format after MSStats PTM site...
MQutil.MaxQToSaintConvert MaxQuant file into a format to work with SAINT
MQutil.MISTformatConvert MaxQuant to MIST format
MQutil.ProteinToSiteConversionConvert Protein format to Site format
MQutil.resultsWideConvert default MSStat results file to Wide format.
MQutil.sampleQuantAdd Abundancd data to Results.
MQutil.SILACToLongConvert the SILAC evidence file to MSstats format
MQutil.spectralCountsGet Spectral Counts
msstats_summarySummarize the MSStats results and data quantification
ph_evidenceMaxQuant Phosphorylation evidence file
ph_keysKeys file: Experimental design describing the 'ph_evidence'...
plotHeatHeatmap of significant values
prettyPrintHeatmapLabelsPretty Labels for Heatmaps
randomDFRandom data set
read_evidence_fileRead the Evidence File
removeMaxQProteinGroupsRemove protein groups
resultsHeatmapCreate Heatmap from MSStat Results
resultsWideConvert default MSStat results file to Wide format.
runMSstatsRun MSstats
sampleCorrelationHeatmapCorrelation heatmaps of all the individual features
samplePeptideBarplotBarplot of peptide counts per biological replicate
select_refSelect Reference protein(s) for normalization
significantHitsSelect significant hits
trimRemove white spaces
volcanoPlotVolcano plot (log2fc / pvalues)
writeContrastGenerate the contrast matrix required by MSstats from a txt...
writeExtrasWrite extras
kroganlab/artMS documentation built on Aug. 17, 2018, 5:31 a.m.