script1: Extract features and generate pairwise alignments.

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

Description

Extract features and generate pairwise alignments.

Usage

script1(
  dataPath,
  outFile = "DIAlignR",
  params = paramsDIAlignR(),
  oswMerged = TRUE,
  runs = 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.
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)
file.remove(file.path(dataPath, "testDIAlignR_script1.RData"))

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.