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]