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Read and Filter Phosphorylation Data for a Specific Sample

Source: R/helper.R
readOnePhos.Rd

readOnePhos reads phosphorylation data from an input table, filters it based on localization probability, score difference, and intensity, and returns the filtered data for a specific sample.

Usage

readOnePhos(
  inputTab,
  sampleName,
  localProbCut = 0.75,
  scoreDiffCut = 5,
  multiMap
)

Arguments

inputTab

A data.table or data.frame containing phosphorylation data with columns for localization probability, score difference, and intensity for various samples.

sampleName

A character string specifying the sample name to filter data for.

localProbCut

A numeric value specifying the cutoff for localization probability. Default is 0.75.

scoreDiffCut

A numeric value specifying the cutoff for score difference. Default is 5.

multiMap

A logical value indicating whether to allow multiple mapping (not used in this function but could be relevant for further extensions).

Value

A data.frame containing the filtered phosphorylation data for the specified sample, with columns for intensity, Uniprot ID, gene name, position within proteins, amino acid residue, and sequence window.

Details

The function filters the input phosphorylation data based on three criteria: localization probability, score difference, and intensity. Only rows that meet or exceed the specified cutoffs for these criteria and have non-zero intensity are retained. The filtered data is then returned with a unique identifier for each row.