alignTargetedRuns: Outputs intensities for each analyte from aligned Targeted-MS...

In shubham1637/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Outputs intensities for each analyte from aligned Targeted-MS runs

Description

This function expects osw and xics directories at dataPath. It first reads osw files and fetches chromatogram indices for each analyte. It then align XICs of its reference XICs. Best peak, which has lowest m-score, about the aligned retention time is picked for quantification.

Usage

alignTargetedRuns(
  dataPath,
  outFile = "DIAlignR",
  params = paramsDIAlignR(),
  oswMerged = TRUE,
  scoreFile = NULL,
  runs = NULL,
  peps = NULL,
  refRun = NULL,
  applyFun = lapply,
  saveAlignedPeaks = FALSE
)

Arguments

dataPath	(string) path to xics and osw directory.
outFile	(string) name of the output file.
params	(list) parameters are entered as list. Output of the paramsDIAlignR function.
oswMerged	(logical) TRUE if merged file from pyprophet is used.
scoreFile	(string) path to the peptide score file, needed when oswMerged is FALSE.
runs	(string) names of xics file without extension.
peps	(integer) ids of peptides to be aligned. If NULL, align all peptides.
refRun	(string) reference for alignment. If no run is provided, m-score is used to select reference run.
applyFun	(function) value must be either lapply or BiocParallel::bplapply.
saveAlignedPeaks	(logical) Save a mapping table to track aligned feature ids against reference feature id

Value

An output table with following columns: precursor, run, intensity, RT, leftWidth, rightWidth, peak_group_rank, m_score, alignment_rank, peptide_id, sequence, charge, group_label.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-14

References

Gupta S, Ahadi S, Zhou W, Röst H. "DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics." Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: https://doi.org/10.1074/mcp.TIR118.001132 Epub 2019 Jan 31.

See Also

getRunNames, getFeatures, setAlignmentRank, getMultipeptide

Examples

params <- paramsDIAlignR()
params[["context"]] <- "experiment-wide"
dataPath <- system.file("extdata", package = "DIAlignR")
BiocParallel::register(BiocParallel::MulticoreParam(workers = 4, progressbar = TRUE))
alignTargetedRuns(dataPath, outFile = "testDIAlignR", params = params, applyFun = BiocParallel::bplapply)

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.