| getXICs {DIAlignR} | R Documentation |
For all the analytes requested in runs, it first creates oswFiles, then, fetches chromatogram indices from oswFiles and extract chromatograms from mzML files.
getXICs(analytes, runs, dataPath = ".", maxFdrQuery = 1, XICfilter = "sgolay", SgolayFiltOrd = 4, SgolayFiltLen = 9, runType = "DIA_proteomics", oswMerged = TRUE, nameCutPattern = "(.*)(/)(.*)", analyteInGroupLabel = FALSE)
analytes |
(string) An analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file. |
runs |
(A vector of string) Names of mzml file without extension. Vector must have names as shown in the example. |
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. |
A list of list. Each list contains XIC-group for that run. XIC-group is a list of dataframe that 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")
runs <- c("hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt",
"hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")
XICs <- getXICs(analytes = c("QFNNTDIVLLEDFQK_3"), runs = runs, dataPath = dataPath)