getPrecursorIndices: Get MS1 chromatogram indices of precursors.

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

Get MS1 chromatogram indices of precursors.

Description

This function reads the header of chromatogram files. It then fetches chromatogram indices by matching transition_group_id(osw) with chromatogramID(xics).

Usage

getPrecursorIndices(
  fileInfo,
  precursors,
  mzPntrs,
  ions = ".*",
  applyFun = lapply
)

Arguments

fileInfo	(data-frame) Output of getRunNames function.
precursors	(data-frame) Atleast two columns transition_group_id and transition_ids are required.
mzPntrs	A list of mzRpwiz.
ions	(character) Strings to specify ions. eg. i0, i1.
applyFun	(function) value must be either lapply or BiocParallel::bplapply.

Value

(list) A list of dataframes having following columns:

transition_group_id	(string) it is PRECURSOR.ID from osw file.
chromatogramIndex	(integer) index of MS1 chromatogram in mzML file.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2022) + GPL-3 Date: 2022-01-15

See Also

chromatogramIdAsInteger, mapPrecursorToChromIndices

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath = dataPath)
precursors <- getPrecursors(fileInfo, oswMerged = TRUE, context = "experiment-wide")
mzPntrs <- getMZMLpointers(fileInfo)
prec2chromIndex <- getPrecursorIndices(fileInfo, precursors, mzPntrs)
for(mz in mzPntrs) DBI::dbDisconnect(mz)

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