groupComparisonTMTPTM: Model PTM and/or protein data and make adjustments if needed

In devonjkohler/MSstatsTMTPTM: Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Description

Takes summarized PTM data from proteinSummarization and models with groupComparisonTMT. Can also take protein level data in the same format and model with groupComparisonTMT. Including protein data allows for adjusting PTM Fold Change by the change in protein abundance without modification.

Usage

groupComparisonTMTPTM(
  data.ptm,
  data.protein = NULL,
  contrast.matrix = "pairwise",
  moderated = FALSE,
  adj.method = "BH"
)

Arguments

data.ptm	Name of the output of the MSstatsTMT proteinSummarization function with PTM data. It should have columns named Protein, TechRepMixture, Mixture, Run, Channel, Condition, BioReplicate, Abundance.
data.protein	Protein dataset returned by the MSstatsTMT proteinSummarization function
contrast.matrix	Comparison between conditions of interests. 1) default is 'pairwise', which compare all possible pairs between two conditions. 2) Otherwise, users can specify the comparisons of interest. Based on the levels of conditions, specify 1 or -1 to the conditions of interests and 0 otherwise. The levels of conditions are sorted alphabetically.
moderated	TRUE will moderate t statistic; FALSE (default) uses ordinary t statistic.
adj.method	Adjusted method for multiple comparison. "BH" is default.

Value

A list models of all modeled and adjusted datasets

Examples

# Load summarized datasets from MSstatsTMT proteinSummarization function
data(quant.msstats.ptm)
data(quant.msstats.protein)

# Load specific contrast matrix
data(example.contrast.matrix)

model.results.contrast <- groupComparisonTMTPTM(data.ptm=quant.msstats.ptm,
                                      data.protein=quant.msstats.protein,
                                      contrast.matrix = example.contrast.matrix)

devonjkohler/MSstatsTMTPTM documentation built on Oct. 27, 2021, 7:50 a.m.