plotAnalyteXICs {DIAlignR} | R Documentation

## Plot extracted-ion chromatogram.

### Description

Plot extracted-ion chromatogram.

### Usage

    plotAnalyteXICs(
      analyte,
      run,
      dataPath = ".",
      maxFdrQuery = 1,
      XICfilter = "sgolay",
      polyOrd = 4,
      kernelLen = 9,
      runType = "DIA_Proteomics",
      oswMerged = TRUE,
      peakAnnot = NULL,
      Title = NULL
    )

### Arguments

`analyte` | (integer) an analyte is a PRECURSOR.ID from the osw file.
`run` | (string) Name of a xics file without extension.
`dataPath` | (string) path to xics 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) must be either sgolay, boxcar, gaussian, loess or none.
`polyOrd` | (integer) order of the polynomial to be fit in the kernel.
`kernelLen` | (integer) number of data-points to consider in the kernel.
`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.
`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

### See Also

`plotXICgroup`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    run <- "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt"
    plotAnalyteXICs(analyte = 2474L, run, dataPath = dataPath, oswMerged = TRUE, XICfilter = "none")
    plotAnalyteXICs(analyte = 2474L, run, dataPath = dataPath, oswMerged = TRUE, XICfilter = "sgolay")

[Package DIAlignR version 2.2.0 Index]