Description Usage Arguments Value Author(s) See Also Examples
Provides the reference run based on lowest p-value.
1 |
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
1 2 3 4 5 6 7 8 9 | 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)
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