getChromatogramIndices: Get chromatogram indices of precursors.

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

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

Usage

getChromatogramIndices(fileInfo, precursors, mzPntrs)

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.

Value

(list) A list of dataframes having following columns:

transition_group_id	(string) it is either fetched from PRECURSOR.GROUP_LABEL or a combination of PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
chromatogramIndex	(integer) Index of chromatogram in mzML file.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-04-07

See Also

chromatogramIdAsInteger, mapPrecursorToChromIndices

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- DIAlignR::getRunNames(dataPath = dataPath)
precursors <- getPrecursors(fileInfo, oswMerged = TRUE)
mzPntrs <- getMZMLpointers(fileInfo)
prec2chromIndex <- getChromatogramIndices(fileInfo, precursors, mzPntrs)
rm(mzPntrs)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.