import2dDataset {TPP2D} | R Documentation

## Import 2D-TPP dataset using a config table

### Description

Import 2D-TPP dataset using a config table

### Usage

    import2dDataset(
      configTable,
      data,
      idVar = "representative",
      intensityStr = "sumionarea_protein_",
      fcStr = "rel_fc_protein_",
      nonZeroCols = "qssm",
      geneNameVar = "clustername",
      addCol = NULL,
      qualColName = "qupm",
      naStrs = c("NA", "n/d", "NaN"),
      concFactor = 1e+06,
      medianNormalizeFC = TRUE,
      filterContaminants = TRUE
    )

### 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.
`intensityStr` | character string indicating which columns contain raw intensities measurements
`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.
`nonZeroCols` | column like default qssm that should be imported and requested to be non-zero in analyzed data
`geneNameVar` | character string of the column name that describes the gene name of a given protein in the raw data files
`addCol` | character string indicating additional column to import
`qualColName` | character string indicating which column can be used for additional quality criteria when deciding between different non-unique protein identifiers.
`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`.
`concFactor` | numeric value that indicates how concentrations need to be adjusted to yield total unit e.g. default mmol - 1e6
`medianNormalizeFC` | perform median normalization (default: TRUE).
`filterContaminants` | boolean variable indicating whether data should be filtered to exclude contaminants (default: TRUE).

### Value

tidy data frame representing a 2D-TPP dataset

### Examples

    data("config_tab")
    data("raw_dat_list")
    import_df <- import2dDataset(configTable = config_tab,
                                 data = raw_dat_list,
                                 idVar = "protein_id",
                                 intensityStr = "signal_sum_",
                                 fcStr = "rel_fc_",
                                 nonZeroCols = "qusm",
                                 geneNameVar = "gene_name",
                                 addCol = NULL,
                                 qualColName = "qupm",
                                 naStrs = c("NA", "n/d", "NaN"),
                                 concFactor = 1e6,
                                 medianNormalizeFC = TRUE,
                                 filterContaminants = TRUE)

[Package TPP2D version 1.10.0 Index]