tpp2dComputeFoldChanges {TPP} | R Documentation

## Compute 2D-TPP fold changes

### Description

Computes fold changes by calculating fold changes of the sumionarea relative to the reference column.

### Usage

    tpp2dComputeFoldChanges(
      configTable = NULL,
      data,
      intensityStr = NULL,
      fcStr = NULL,
      newFcStr = "rel_fc_"
    )

### Arguments

`configTable` | DEPRECATED
`data` | dataframe that contain the data for the 2D-TPP experiment
`intensityStr` | DEPRECATED
`fcStr` | DEPRECATED
`newFcStr` | character string indicating how columns that will contain the actual fold change values will be called. The suffix `newFcStr` will be pasted in front of the names of the experiments.

### Value

A data.frame with additional columns with constitute fold changes calculated with respect to the intensity values of the zero treatment column

### Examples

    # Preparation:
    data(panobinostat_2DTPP_smallExample)

    # Import data:
    datIn <- tpp2dImport(configTable = panobinostat_2DTPP_config,
                          data = panobinostat_2DTPP_data,
                          idVar = "representative",
                          addCol = "clustername",
                          intensityStr = "sumionarea_protein_",
                          nonZeroCols = "qusm")

    # View attributes of imported data (experiment infos and import arguments):
    attr(datIn, "importSettings") %>% unlist
    attr(datIn, "configTable")

    # Compute fold changes:
    datFC <- tpp2dComputeFoldChanges(data = datIn)

    # View updated attributes. Now contain field 'fcStrNorm' indicating prefix
    # of the fold change columns after normalization.
    attr(datFC, "importSettings")["fcStr"]

[Package TPP version 3.16.5 Index]