annotateDataList: Annotate imported data list using a config table

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

Annotate imported data list using a config table

Description

Annotate imported data list using a config table

Usage

annotateDataList(dataList, geneNameVar, configLong, intensityStr, fcStr)

Arguments

dataList	list of datasets from different MS runs corresponding to a 2D-TPP dataset
geneNameVar	character string of the column name that describes the gene name of a given protein in the raw data files
configLong	long formatted data frame of a corresponding config table
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.

Value

data frame containing all data annotated by information supplied in the config table

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")
configLong <- configWide2Long(configWide = config_tab)
annotateDataList(dataList = dataList,
                 geneNameVar = "gene_name",
                 configLong = configLong,
                 intensityStr = "signal_sum_",
                 fcStr = "rel_fc_")

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