annotateDataList: Annotate imported data list using a config table

View source: R/import_funcs.R

annotateDataListR Documentation

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.