plotAnalyteXICs {DIAlignR} | R Documentation |
Plot extracted-ion chromatogram.
plotAnalyteXICs( analyte, run, dataPath = ".", maxFdrQuery = 1, XICfilter = "sgolay", polyOrd = 4, kernelLen = 9, runType = "DIA_proteomics", oswMerged = TRUE, peakAnnot = NULL, Title = NULL )
analyte |
(integer) an analyte is a PRECURSOR.ID from the osw file. |
run |
(string) Name of a mzml file without extension. |
dataPath |
(string) 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) 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. |
A plot to the current device.
Shubham Gupta, shubh.gupta@mail.utoronto.ca
ORCID: 0000-0003-3500-8152
License: (c) Author (2019) + GPL-3 Date: 2019-12-13
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")