import2dDataset: Import 2D-TPP dataset using a config table

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

Import 2D-TPP dataset using a config table

Description

Import 2D-TPP dataset using a config table

Usage

import2dDataset(
  configTable,
  data,
  idVar = "representative",
  intensityStr = "sumionarea_protein_",
  fcStr = "rel_fc_protein_",
  nonZeroCols = "qssm",
  geneNameVar = "clustername",
  addCol = NULL,
  qualColName = "qupm",
  naStrs = c("NA", "n/d", "NaN"),
  concFactor = 1e+06,
  medianNormalizeFC = TRUE,
  filterContaminants = TRUE
)

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.
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.
nonZeroCols	column like default qssm that should be imported and requested to be non-zero in analyzed data
geneNameVar	character string of the column name that describes the gene name of a given protein in the raw data files
addCol	character string indicating additional column to import
qualColName	character string indicating which column can be used for additional quality criteria when deciding between different non-unique protein identifiers.
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.
concFactor	numeric value that indicates how concentrations need to be adjusted to yield total unit e.g. default mmol - 1e6
medianNormalizeFC	perform median normalization (default: TRUE).
filterContaminants	boolean variable indicating whether data should be filtered to exclude contaminants (default: TRUE).

Value

tidy data frame representing a 2D-TPP dataset

Examples

data("config_tab")
data("raw_dat_list")
import_df <- import2dDataset(configTable = config_tab, 
                             data = raw_dat_list,
                             idVar = "protein_id",
                             intensityStr = "signal_sum_",
                             fcStr = "rel_fc_",
                             nonZeroCols = "qusm",
                             geneNameVar = "gene_name",
                             addCol = NULL,
                             qualColName = "qupm",
                             naStrs = c("NA", "n/d", "NaN"),
                             concFactor = 1e6,
                             medianNormalizeFC = TRUE,
                             filterContaminants = TRUE)

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