MaxQtoMSstatsTMTFormat: Generate MSstatsTMT required input format from MaxQuant...

In huang704/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Description

Convert MaxQuant output into the required input format for MSstatsTMT.

Usage

MaxQtoMSstatsTMTFormat(
  evidence,
  proteinGroups,
  annotation,
  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, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition. Refer to the example 'annotation.mq' for the meaning of each column.
which.proteinid	Use 'Proteins'(default) column for protein name. 'Leading.proteins' or 'Leading.razor.proteins' or 'Gene.names' can be used instead to get the protein ID with single protein. 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)

huang704/MSstatsTMT documentation built on Jan. 1, 2021, 3:21 a.m.