getXICs4AlignObj: Extract XICs of analytes

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

Description

For all the analytes requested, it fetches chromatogram indices from prec2chromIndex and extracts chromatograms using mzPntrs.

Usage

getXICs4AlignObj(mzPntrs, fileInfo, runs, prec2chromIndex, analytes)

Arguments

mzPntrs	a list of mzRpwiz.
fileInfo	(data-frame) output of getRunNames().
runs	(vector of string) names of mzML files without extension.
prec2chromIndex	(list of data-frames) output of getChromatogramIndices(). Each dataframe has two columns: transition_group_id and chromatogramIndex.
analytes	(integer) a vector of precursor IDs.

Value

A list of list of data-frames. Each data frame has elution time and intensity of fragment-ion XIC.

Author(s)

Shubham Gupta, [e-mail]

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

See Also

getChromatogramIndices, getRunNames

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",
          "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt")
analytes <- c(32L, 898L, 2474L)
params <- paramsDIAlignR()
params[["chromFile"]] <- "mzML"
fileInfo <- getRunNames(dataPath = dataPath)
fileInfo <- updateFileInfo(fileInfo, runs)
precursors <- getPrecursorByID(analytes,fileInfo)
mzPntrs <- getMZMLpointers(fileInfo)
prec2chromIndex <- getChromatogramIndices(fileInfo, precursors, mzPntrs)
XICs <- getXICs4AlignObj(mzPntrs, fileInfo, runs, prec2chromIndex, analytes)
rm(mzPntrs)

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