getXICs {DIAlignR} | R Documentation

## Get XICs of all analytes

### 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, 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

    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)

[Package DIAlignR version 2.2.0 Index]