getChromatogramIndices {DIAlignR} | R Documentation

## Get chromatogram indices of precursors.

### Description

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

### Usage

    getChromatogramIndices(fileInfo, precursors, mzPntrs, 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.
`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 chromatogram in mzML file.

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

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 <- getRunNames(dataPath = dataPath)
    precursors <- getPrecursors(fileInfo, oswMerged = TRUE, context = "experiment-wide")
    mzPntrs <- getMZMLpointers(fileInfo)
    prec2chromIndex <- getChromatogramIndices(fileInfo, precursors, mzPntrs)
    for(mz in mzPntrs) DBI::dbDisconnect(mz)

[Package DIAlignR version 2.2.0 Index]