tpptrTidyUpESets: Tidy up expressionSets

In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Description

Convert list of expressionSets (intermediate output of several TPP-TR functions) to tidy tables.

Usage

tpptrTidyUpESets(tppESetList, returnType = "exprs")

Arguments

tppESetList	A list of expressionSets, returned by most TPP-TR functions.
returnType	A string with two possible values: "exprs", "featureData".

Details

expressionSet lists are for example produced by tpptrImport, tpptrNormalize, tpptrCurveFit.

Value

Either the fold changes per protein across all experiments (if returnType = "exprs"), or the additional annotation per protein and experiment (if returnType = "featureData"). For example, the peptide counts per identified protein can be found here.

Examples

data(hdacTR_smallExample)
tpptrData <- tpptrImport(configTable = hdacTR_config, data = hdacTR_data)
concentrations <- tpptrTidyUpESets(tpptrData)
additionalInfos <- tpptrTidyUpESets(tpptrData, returnType = "featureData")
summary(concentrations)

DoroChilds/TPP documentation built on Oct. 31, 2021, 4:38 a.m.