getAnalytes {DIAlignR}R Documentation

Get names of analytes found in all runs.

Description

Get names of analytes found in all runs.

Usage

getAnalytes(dataPath, runs = NULL, oswMerged = TRUE,
  runType = "DIA_Proteomics", commonAnalytes = FALSE,
  maxFdrQuery = 0.05, nameCutPattern = "(.*)(/)(.*)",
  analyteInGroupLabel = FALSE)

Arguments

dataPath

(char) Path to mzml and osw directory.

runs

(A vector of string) Names of mzml file without extension.

oswMerged

(logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.

runType

(char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".

commonAnalytes

(logical) TRUE: intersect across all runs, FASLE: union across all runs.

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.

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.

Value

A vector of strings.

Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-14

See Also

getRunNames, getOswAnalytes, getAnalytesName

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
runs <- c("hroest_K120809_Strep0%PlasmaBiolRepl2_R04_SW_filt",
 "hroest_K120809_Strep10%PlasmaBiolRepl2_R04_SW_filt")
analytes <- getAnalytes(dataPath, runs, oswMerged = TRUE, maxFdrQuery = 0.01,
 commonAnalytes = TRUE)
[Package DIAlignR version 0.99.12 Index]