getRefRun {DIAlignR} | R Documentation |
Provides the reference run based on lowest p-value.
getRefRun(peptideScores, applyFun = lapply)
peptideScores |
(list of data-frames) each dataframe has scores of a peptide across all runs. |
applyFun |
(function) value must be either lapply or BiocParallel::bplapply. |
(dataframe) has two columns:
peptide_id |
(integer) a unique id for each peptide. |
run |
(string) run identifier. |
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2020) + GPL-3 Date: 2020-04-08
dataPath <- system.file("extdata", package = "DIAlignR") fileInfo <- getRunNames(dataPath = dataPath) precursorsInfo <- getPrecursors(fileInfo, oswMerged = TRUE, runType = "DIA_Proteomics", context = "experiment-wide", maxPeptideFdr = 0.05) peptideIDs <- unique(precursorsInfo$peptide_id) peptidesInfo <- getPeptideScores(fileInfo, peptideIDs) peptidesInfo <- lapply(peptideIDs, function(pep) peptidesInfo [.(pep),]) names(peptidesInfo) <- as.character(peptideIDs) getRefRun(peptidesInfo)