tppccrTransform {TPP} | R Documentation

## Transform fold changes of TPP-CCR experiment

### 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),]

[Package TPP version 3.20.1 Index]