tpp2dImport {TPP} | R Documentation

## Import 2D-TPP data

### Description

Imports data from 2D-TPP experiments by parsing a configTable and reading in corresponding data file or data frames containing raw data (sumionarea values) and creating a big data frame comprising all samples with respective fold changes

### Usage

    tpp2dImport(
      configTable = NULL,
      data = NULL,
      idVar = "gene_name",
      addCol = NULL,
      intensityStr = "signal_sum_",
      qualColName = "qupm",
      nonZeroCols = "qssm",
      fcStr = NULL
    )

### Arguments

`configTable` | dataframe, or character object with the path to a file, that specifies important details of the 2D-TPP experiment. See Section `details` for instructions how to create this object.
`data` | single dataframe, containing raw measurements and if already available fold changes and additional annotation columns to be imported. Can be used instead of specifying the file path in the `configTable` argument.
`idVar` | character string indicating which data column provides the unique identifiers for each protein.
`addCol` | additional column names that specify columns in the input data that are to be attached to the data frame throughout the analysis
`intensityStr` | character string indicating which columns contain the actual sumionarea values. Those column names containing the suffix `intensityStr` will be regarded as containing sumionarea values.
`qualColName` | character string indicating which column can be used for additional quality criteria when deciding between different non-unique protein identifiers.
`nonZeroCols` | character string indicating a column that will be used for filtering out zero values.
`fcStr` | character string indicating which columns contain the actual fold change values. Those column names containing the suffix `fcStr` will be regarded as containing fold change values.

### Value

A dataframe comprising all experimental data

### 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")

[Package TPP version 3.20.1 Index]