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

Description Usage Arguments Value Examples

View source: R/import_funcs.R

Description

Import 2D-TPP dataset using a config table

Usage

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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

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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)

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