plotAnalyteXICs {DIAlignR} | R Documentation

## Plot extracted-ion chromatogram.

### Description

Plot extracted-ion chromatogram.

### Usage

    plotAnalyteXICs(analyte, run, dataPath = ".", maxFdrQuery = 1,
      XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 9,
      runType = "DIA_proteomics", oswMerged = TRUE,
      nameCutPattern = "(.*)(/)(.*)", analyteInGroupLabel = FALSE,
      peakAnnot = NULL, Title = NULL)

### Arguments

`analyte` | (string) An analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`run` | (string) Name of a mzml file without extension.
`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.
`peakAnnot` | (numeric) Peak-apex time.
`Title` | (logical) TRUE: name of the list will be displayed as title.

### Value

A plot to the current device.

### Author(s)

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

ORCID: 0000-0003-3500-8152

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

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    run <- "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
    plotAnalyteXICs(analyte = "QFNNTDIVLLEDFQK_3", run, dataPath = dataPath, XICfilter = "none")
    plotAnalyteXICs(analyte = "14299_QFNNTDIVLLEDFQK/3", run, dataPath = dataPath,
    XICfilter = "sgolay", analyteInGroupLabel = TRUE)

[Package DIAlignR version 0.99.12 Index]