mstScript2: Performs alignment using mstScript1 output

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

Performs alignment using mstScript1 output

Description

Performs alignment using mstScript1 output

Usage

mstScript2(
  dataPath,
  outFile = "DIAlignR",
  params = paramsDIAlignR(),
  oswMerged = TRUE,
  scoreFile = NULL,
  peps = NULL,
  mstNet = 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.
mstNet	(string) minimum spanning tree in string format. See example of mstScript2.
applyFun	(function) value must be either lapply or BiocParallel::bplapply.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2022) + GPL-3 Date: 2022-04-19

See Also

mstAlignRuns, mstScript1

Examples

params <- paramsDIAlignR()
params[["context"]] <- "experiment-wide"
dataPath <- system.file("extdata", package = "DIAlignR")
BiocParallel::register(BiocParallel::MulticoreParam(workers = 4, progressbar = TRUE))
mstScript1(dataPath, outFile = "testDIAlignR", params = params, applyFun = BiocParallel::bplapply)
mstNet <- "run0 run0\nrun1 run2"
mstScript2(dataPath, outFile = "testDIAlignR", params = params, mstNet = mstNet, applyFun = lapply)
file.remove(file.path(dataPath, "testDIAlignR_mst1.RData"))
file.remove("testDIAlignR.tsv")

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