tppccrTransform {TPP} | R Documentation |
Transform fold changes of TPP-CCR experiment to prepare them for dose response curve fitting.
tppccrTransform(data, fcCutoff = 1.5, fcTolerance = 0.1)
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. |
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
.
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
.
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),]