tpp2dImport: Import 2D-TPP data
In DoroChilds/TPP: Analyze thermal proteome profiling (TPP) experiments

Description Usage Arguments Value Examples

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

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

`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.

A dataframe comprising all experimental data

# 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")