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Read Phosphorylation Data for One Sample from DIA

Source: R/helper.R
readOnePhosDIA.Rd

readOnePhosDIA reads and processes phosphorylation data for a single sample from a DIA experiment, applying filters for localization probability and removing duplicates if specified.

Usage

readOnePhosDIA(inputTab, sampleName, localProbCut = 0.75, removeDup = FALSE)

Arguments

inputTab

A data.table or data.frame containing phosphorylation data.

sampleName

A character string specifying the sample name.

localProbCut

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

removeDup

A logical value indicating whether to remove duplicate entries based on UniprotID and intensity. Default is FALSE.

Value

A data.table containing the processed phosphorylation data for the specified sample.

Details

This function processes phosphorylation data for a single sample by filtering based on localization probability and non-zero intensity. It handles multiplicity by summarizing intensities and optionally removes duplicates. The resulting data is returned as a data.table with unique identifiers.