getXICs4AlignObj {DIAlignR} | R Documentation

## Extract XICs of analytes

### 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, shubh.gupta@mail.utoronto.ca

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)

[Package DIAlignR version 2.2.0 Index]