getXICs: Get XICs of all analytes

Description Usage Arguments Value Author(s) See Also Examples

View source: R/get_peaks_chromatograms.R

Description

For all the analytes requested in runs, it first creates oswFiles, then, fetches chromatogram indices from oswFiles and extract chromatograms from mzML files.

Usage

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getXICs(
  analytes,
  runs,
  dataPath = ".",
  maxFdrQuery = 1,
  runType = "DIA_Proteomics",
  oswMerged = TRUE,
  params = paramsDIAlignR()
)

Arguments

analytes

(integer) a vector of precursor IDs.

runs

(vector of string) names of mzML files without extension.

dataPath

(string) Path to xics 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.

params

(list) parameters are entered as list. Output of the paramsDIAlignR function.

Value

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.

Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

See Also

getXICs4AlignObj, getRunNames, analytesFromFeatures

Examples

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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)

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.