alignTargetedRuns2: Star alignment for few ids

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

Description

Star alignment for few ids

Usage

alignTargetedRuns2(
  dataPath,
  outFile = "DIAlignR.tsv",
  params,
  ids = NULL,
  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	(string) names of xics file without extension.
applyFun	(function) value must be either lapply or BiocParallel::bplapply.

Value

(None)

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2021) + GPL-3 Date: 2021-01-20

See Also

alignTargetedRuns

Examples

## Not run: 
ids <- as.integer(scan(file = "data/ids.txt"))
params <- paramsDIAlignR()
params[["maxFdrQuery"]] <- 1.0
params[["maxPeptideFdr"]] <- 1.0
params[["kernelLen"]] <- 11L
params$globalAlignmentFdr <- 0.001
params[["batchSize"]] <- 1000L
BiocParallel::register(BiocParallel::MulticoreParam(workers = 6, log = FALSE, threshold = "INFO", stop.on.error = TRUE))
alignTargetedRuns2(dataPath = ".", params = params, outFile = "te1.tsv", ids = ids, applyFun = BiocParallel::bplapply)

## End(Not run)

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