getXICs4AlignObj {DIAlignR} | R Documentation |
For all the analytes requested, it fetches chromatogram indices from prec2chromIndex and extracts chromatograms using mzPntrs.
getXICs4AlignObj(mzPntrs, fileInfo, runs, prec2chromIndex, analytes)
mzPntrs |
a list of mzRpwiz. |
fileInfo |
(data-frame) output of getRunNames(). |
runs |
(vector of string) names of mzML files without extension. |
prec2chromIndex |
(list of data-frames) output of getChromatogramIndices(). Each dataframe has two columns: transition_group_id and chromatogramIndex. |
analytes |
(integer) a vector of precursor IDs. |
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
getChromatogramIndices, getRunNames
dataPath <- system.file("extdata", package = "DIAlignR") runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt", "hroest_K120808_Strep10%PlasmaBiolRepl1_R03_SW_filt") analytes <- c(32L, 898L, 2474L) fileInfo <- getRunNames(dataPath = dataPath) fileInfo <- updateFileInfo(fileInfo, runs) precursors <- getPrecursorByID(analytes,fileInfo) mzPntrs <- getMZMLpointers(fileInfo) prec2chromIndex <- getChromatogramIndices(fileInfo, precursors, mzPntrs) XICs <- getXICs4AlignObj(mzPntrs, fileInfo, runs, prec2chromIndex, analytes) rm(mzPntrs)