plotAnalyteXICs: Plot extracted-ion chromatogram.

In Roestlab/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

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")

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.