MaxQtoMSstatsTMTFormat {MSstatsTMT}R Documentation

Generate MSstatsTMT required input format for MaxQuant output

Description

Convert MaxQuant output into the required input format for MSstatsTMT.

Usage

MaxQtoMSstatsTMTFormat(evidence, proteinGroups, annotation, fraction = FALSE,
  which.proteinid = "Proteins", rmProt_Only.identified.by.site = FALSE,
  useUniquePeptide = TRUE, rmPSM_withMissing_withinRun = FALSE,
  rmPSM_withfewMea_withinRun = TRUE, rmProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum)

Arguments

evidence

name of 'evidence.txt' data, which includes feature-level data.

proteinGroups

name of 'proteinGroups.txt' data.

annotation

data frame which contains column Run, Channel, Condition, BioReplicate, Mixture.

fraction

indicates whether the data has fractions. If there are fractions, then overlapped peptide ions will be removed and then fractions are combined for each mixture.

which.proteinid

Use 'Proteins'(default) column for protein name. 'Leading.proteins' or 'Leading.razor.proteins' can be used instead. However, those can potentially have the shared peptides.

rmProt_Only.identified.by.site

TRUE will remove proteins with '+' in 'Only.identified.by.site' column from proteinGroups.txt, which was identified only by a modification site. FALSE is the default.

useUniquePeptide

TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.

rmPSM_withMissing_withinRun

TRUE will remove PSM with any missing value within each Run. Defaut is FALSE.

rmPSM_withfewMea_withinRun

only for rmPSM_withMissing_withinRun = FALSE. TRUE(default) will remove the features that have 1 or 2 measurements within each Run.

rmProtein_with1Feature

TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.

summaryforMultipleRows

sum(default) or max - when there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.

Value

input for proteinSummarization function

Examples

head(evidence)
head(proteinGroups)
head(annotation.mq)
input.mq <- MaxQtoMSstatsTMTFormat(evidence, proteinGroups, annotation.mq)
head(input.mq)

[Package MSstatsTMT version 1.2.0 Index]