mstScript1: Extract features and generate minimum spanning tree.

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

Extract features and generate minimum spanning tree.

Description

Extract features and generate minimum spanning tree.

Usage

mstScript1(
  dataPath,
  outFile = "DIAlignR",
  params = paramsDIAlignR(),
  oswMerged = TRUE,
  runs = 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.
runs	(string) names of xics file without extension.
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, mstScript2

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)
file.remove(file.path(dataPath, "testDIAlignR_mst1.RData"))

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.