script2: Performs alignment using script1 output

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

Performs alignment using script1 output

Description

Performs alignment using script1 output

Usage

script2(
  dataPath,
  outFile = "DIAlignR",
  params = paramsDIAlignR(),
  oswMerged = TRUE,
  scoreFile = NULL,
  peps = NULL,
  refRun = NULL,
  applyFun = lapply
)

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.
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.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-02-20

See Also

alignTargetedRuns

Examples

params <- paramsDIAlignR()
params[["context"]] <- "experiment-wide"
dataPath <- system.file("extdata", package = "DIAlignR")
BiocParallel::register(BiocParallel::MulticoreParam(workers = 4, progressbar = TRUE))
script1(dataPath, outFile = "testDIAlignR", params = params, applyFun = BiocParallel::bplapply)
script2(dataPath, outFile = "testDIAlignR", params = params, applyFun = lapply)
file.remove(file.path(dataPath, "testDIAlignR_script1.RData"))

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