import2dMain: Import 2D-TPP dataset main function

In nkurzaw/TPP2D: Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)

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")

nkurzaw/TPP2D documentation built on May 9, 2023, 10:04 a.m.