script2: Performs alignment using script1 output

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

Description

Performs alignment using script1 output

Usage

script2(
  dataPath,
  outFile = "DIAlignR",
  params = paramsDIAlignR(),
  oswMerged = TRUE,
  runs = 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 for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
runs	(a vector of string) names of xics file without extension.
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"))

Roestlab/DIAlignR documentation built on March 3, 2021, 9:09 a.m.