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, runType = "DIA_proteomics", oswMerged = TRUE )
analytes |
(integer) a vector of precursor IDs. |
runs |
(vector of string) names of mzML files 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. |
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. |
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
getXICs4AlignObj, getRunNames, analytesFromFeatures
dataPath <- system.file("extdata", package = "DIAlignR") runs <- c("hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt", "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt") analytes <- c(32L, 898L, 2474L) XICs <- getXICs(analytes, runs = runs, dataPath = dataPath)