getXICs {DIAlignR} | R Documentation

## Get XICs of all analytes

### Description

For all the analytes requested in runs, it first creates oswFiles, then, fetches chromatogram indices from oswFiles and extract chromatograms from mzML files.

### Usage

    getXICs(analytes, runs, dataPath = ".", maxFdrQuery = 1,
      XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 9,
      runType = "DIA_proteomics", oswMerged = TRUE,
      nameCutPattern = "(.*)(/)(.*)", analyteInGroupLabel = FALSE)

### Arguments

`analytes` | (string) An analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`runs` | (A vector of string) Names of mzml file without extension. Vector must have names as shown in the example.
`dataPath` | (char) Path to mzml and osw directory.
`maxFdrQuery` | (numeric) A numeric value between 0 and 1. It is used to filter features from osw file which have SCORE_MS2.QVALUE less than itself.
`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.
`runType` | (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
`oswMerged` | (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`nameCutPattern` | (string) regex expression to fetch mzML file name from RUN.FILENAME columns of osw files.
`analyteInGroupLabel` | (logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.

### Value

A list of list. Each list contains XIC-group for that run. XIC-group is a list of dataframe that 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")
    runs <- c("hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt",
     "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")
    XICs <- getXICs(analytes = c("QFNNTDIVLLEDFQK_3"), runs = runs, dataPath = dataPath)

[Package DIAlignR version 0.99.12 Index]