import2dMain {TPP2D} | R Documentation |
Import 2D-TPP dataset main function
import2dMain( configTable, data, idVar, fcStr, addCol, naStrs, intensityStr, qualColName, nonZeroCols )
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 |
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
|
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 |
list of data frames containing different datasets
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")