| getXICs4AlignObj {DIAlignR} | R Documentation |
For all the analytes requested, it fetches chromatogram indices from oswFiles and extract chromatograms from mzML files.
getXICs4AlignObj(dataPath, runs, oswFiles, analytes, XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 9, mzPntrs = NULL)
dataPath |
(char) path to mzml and osw directory. |
runs |
(vector of string) names of mzML files without extension. Names of the vector must be a combination of "run" and an iteger e.g. "run2". |
oswFiles |
(list of data-frames) it is output from getOswFiles function. |
analytes |
(string) analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file. |
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. |
mzPntrs |
A list of mzRpwiz. |
A list of list of data-frames. Each data frame has elution time and intensity of fragment-ion XIC.
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")
filenames <- DIAlignR::getRunNames(dataPath = dataPath)
runs <- c("run1" = "hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",
"run0" = "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt")
oswFiles <- DIAlignR::getOswFiles(dataPath, filenames)
analytes <- "QFNNTDIVLLEDFQK_3"
XICs <- getXICs4AlignObj(dataPath, runs, oswFiles, analytes)