progAlignRuns2: Progressive alignment for few ids

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

Description

Progressive alignment for few ids

Usage

progAlignRuns2(
  dataPath,
  params,
  outFile = "DIAlignR.tsv",
  ropenms,
  ids = NULL,
  oswMerged = TRUE,
  runs = NULL,
  newickTree = NULL,
  applyFun = lapply
)

Arguments

dataPath	(string) path to xics and osw directory.
params	(list) parameters are entered as list. Output of the paramsDIAlignR function.
outFile	(string) name of the output file.
ropenms	(pyopenms module) get this python module through get_ropenms. Required only for chrom.mzML files.
oswMerged	(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
runs	(string) names of xics file without extension.
newickTree	(string) guidance tree in newick format. Look up getTree.
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

progAlignRuns

Examples

## Not run: 
ids <- as.integer(scan(file = "data/ids.txt"))
params <- paramsDIAlignR()
params[["maxFdrQuery"]] <- 1.0
params[["maxPeptideFdr"]] <- 1.0
params[["kernelLen"]] <- 11
params$batchSize <- 10000L
params$globalAlignmentFdr <- 0.001
BiocParallel::register(BiocParallel::MulticoreParam(workers = 6, log = FALSE, threshold = "INFO", stop.on.error = TRUE))
ropenms <- get_ropenms(condaEnv = "TricEnvr")
progAlignRuns2(dataPath = ".", params = params, outFile = "prog.tsv", ropenms = ropenms, ids = ids, applyFun = BiocParallel::bplapply)

## End(Not run)

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