tppccrTransform: Transform fold changes of TPP-CCR experiment

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

Description

Transform fold changes of TPP-CCR experiment to prepare them for dose response curve fitting.

Usage

tppccrTransform(data, fcCutoff = 1.5, fcTolerance = 0.1)

Arguments

data	expressionSet object containing the data to be transformed.
fcCutoff	cutoff for highest compound concentration fold change.
fcTolerance	tolerance for the fcCutoff parameter. See details.

Details

Only proteins with fold changes bigger than [fcCutoff * (1 - fcTolerance) or smaller than 1/(fcCutoff * (1 - fcTolerance))] will be used for curve fitting. Additionally, the proteins fulfilling the fcCutoff criterion without tolerance will be marked in the output column meets_FC_requirement.

Value

List of expressionSet objects storing the transformed fold changes, as well as row and column metadata. In each expressionSet S, the fold changes can be accessed by Biobase::exprs(S). Protein expNames can be accessed by featureNames(S). Isobaric labels and the corresponding concentrations are returned by S$label and S$concentration.

Examples

data(hdacCCR_smallExample)
tppccrData <- tppccrImport(configTable=hdacCCR_config, data = hdacCCR_data)
tppccrNorm <- tppccrNormalize(data=tppccrData)
# Perform transformation:
tppccrTransformed <- tppccrTransform(data=tppccrNorm)
# Obtain transformed measurements per replicate:
transf_replicate1 <- tppccrTransformed$Panobinostat_1
transf_replicate2 <- tppccrTransformed$Panobinostat_2
# Inspect transformed data in replicate 1:
effects_replicate1 <- Biobase::featureData(transf_replicate1)$compound_effect
newData_repl1 <- data.frame(Biobase::exprs(transf_replicate1), 
                              Type=effects_replicate1)[!is.na(effects_replicate1),]
                              

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