getXICs: Get XICs of all analytes

In Roestlab/DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

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

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, [e-mail]

ORCID: 0000-0003-3500-8152

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

See Also

getXICs4AlignObj, getRunNames, analytesFromFeatures

Examples

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/DIAlignR documentation built on March 3, 2021, 9:09 a.m.