getXICs4AlignObj {DIAlignR} | R Documentation

## Extract XICs of all analytes from oswFiles

### Description

For all the analytes requested, it fetches chromatogram indices from oswFiles and extract chromatograms from mzML files.

### Usage

    getXICs4AlignObj(dataPath, runs, oswFiles, analytes,
      XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 9,
      mzPntrs = NULL)

### Arguments

`dataPath` | (char) path to mzml and osw directory.
`runs` | (vector of string) names of mzML files without extension. Names of the vector must be a combination of "run" and an iteger e.g. "run2".
`oswFiles` | (list of data-frames) it is output from getOswFiles function.
`analytes` | (string) analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`XICfilter` | (string) this must be one of the strings "sgolay", "none".
`SgolayFiltOrd` | (integer) it defines the polynomial order of filer.
`SgolayFiltLen` | (integer) must be an odd number. It defines the length of filter.
`mzPntrs` | A list of mzRpwiz.

### 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

`getOswFiles, getRunNames`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    filenames <- DIAlignR::getRunNames(dataPath = dataPath)
    runs <- c("run1" = "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",
              "run0" =  "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt")
    oswFiles <- DIAlignR::getOswFiles(dataPath, filenames)
    analytes <- "QFNNTDIVLLEDFQK_3"
    XICs <- getXICs4AlignObj(dataPath, runs, oswFiles, analytes)

[Package DIAlignR version 0.99.12 Index]