progAlignRuns: Peptide quantification through progressive alignment

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

Peptide quantification through progressive alignment

Description

This function expects osw and xics directories at dataPath. It first reads osw files and fetches chromatogram indices for each analyte. To perform alignment, first a crude guide-tree is built which can also be provided with newickTree parameter. As we traverse from the leaf-nodes to the root node, runs are aligned pairwise. The root node is named master1 that has average of all fragment ion chromatograms and identified peak-groups. These features are propagated back to leaf nodes and finally aligned features are written in the output file.

Usage

progAlignRuns(
  dataPath,
  params,
  outFile = "DIAlignR",
  ropenms = NULL,
  oswMerged = TRUE,
  scoreFile = NULL,
  runs = NULL,
  peps = 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 if merged file from pyprophet is used.
scoreFile	(string) path to the peptide score file, needed when oswMerged is FALSE.
runs	(string) names of xics file without extension.
peps	(integer) ids of peptides to be aligned. If NULL, align all peptides.
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 (2020) + GPL-3 Date: 2020-07-10

See Also

alignTargetedRuns

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
params <- paramsDIAlignR()
params[["context"]] <- "experiment-wide"
## Not run: 
ropenms <- get_ropenms(condaEnv = "envName")
progAlignRuns(dataPath, params = params, outFile = "test3", ropenms = ropenms)
# Removing aligned vectors
file.remove(list.files(dataPath, pattern = "*_av.rds", full.names = TRUE))
# Removing temporarily created master chromatograms
file.remove(list.files(file.path(dataPath, "xics"), pattern = "^master[A-Za-z0-9]+\\.chrom\\.sqMass$", full.names = TRUE))
file.remove(file.path(dataPath, "test3.temp.RData"))
file.remove(file.path(dataPath, "master.merged.osw"))

## End(Not run)

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