import2dMain: Import 2D-TPP dataset main function

Description Usage Arguments Value Examples

View source: R/import_funcs.R

Description

Import 2D-TPP dataset main function

Usage

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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

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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")

TPP2D documentation built on Nov. 8, 2020, 4:54 p.m.