import2dMain {TPP2D} | R Documentation

## Import 2D-TPP dataset main function

### Description

Import 2D-TPP dataset main function

### Usage

    import2dMain(configTable, data, idVar, fcStr, addCol, naStrs, intensityStr,
      qualColName, nonZeroCols)

### Arguments

`configTable` | character string of a file path to a config table
`data` | possible list of datasets from different MS runs corresponding to a 2D-TPP dataset, circumvents loading datasets referencend in config table, default is NULL
`idVar` | character string indicating which data column provides the unique identifiers for each protein.
`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.
`addCol` | character string indicating additional column to import
`naStrs` | character vector indicating missing values in the data table. When reading data from file, this value will be passed on to the argument `na.strings` in function `read.delim`.
`intensityStr` | character string indicating which columns contain raw intensities measurements
`qualColName` | character string indicating which column can be used for additional quality criteria when deciding between different non-unique protein identifiers.
`nonZeroCols` | column like default qssm that should be imported and requested to be non-zero in analyzed data

### Value

list of data frames containing different datasets

### Examples

    data("config_tab")
    data("raw_dat_list")
    dataList <- import2dMain(configTable = config_tab,
                             data = raw_dat_list,
                             idVar = "protein_id",
                             fcStr = "rel_fc_",
                             addCol = "gene_name",
                             naStrs = NA,
                             intensityStr = "signal_sum_",
                             nonZeroCols = "qusm",
                             qualColName = "qupm")

[Package TPP2D version 1.4.1 Index]