getOswFiles {DIAlignR} | R Documentation

## Get list of peptides and their chromatogram indices.

### Description

This function reads all osw and xics files in the directories at dataPath. It selects analytes which has associated features with m-score < maxFdrQuery. For these analytes it fetches chromatogram indices by matching transition_id(osw) with chromatogramID(xics).

### Usage

    getOswFiles(
      fileInfo,
      mzPntrs,
      maxFdrQuery = 0.05,
      analyteFDR = 0.01,
      oswMerged = TRUE,
      analytes = NULL,
      runType = "DIA_Proteomics",
      analyteInGroupLabel = FALSE
    )

### Arguments

`mzPntrs` | A list of mzRpwiz. FALSE for fetching analytes as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`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.
`analyteFDR` | (numeric) Not used.
`oswMerged` | (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`analytes` | (string) analyte is as PRECURSOR.GROUP_LABEL or as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`runType` | (char) This must be one of the strings "DIA_Proteomics", "DIA_Metabolomics".
`analyteInGroupLabel` | (logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file.
`dataPath` | (char) path to xics and osw directory.
`filenames` | (data-frame) column "filename" contains RUN table from osw files. column "runs" contain respective mzML names without extension. To get filenames use DIAlignR::getRunNames function.

### Value

(data-frames) Data-frame has following columns:

`transition_group_id` | (string) it is either fetched from PRECURSOR.GROUP_LABEL or a combination of PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.
`RT` | (numeric) retention time as in FEATURE.EXP_RT of osw files.
`delta_rt` | (numeric) as in FEATURE.DELTA_RT of osw files.
`assay_RT` | (numeric) library retention time as in PRECURSOR.LIBRARY_RT of osw files.
`Intensity` | (numeric) peak intensity as in FEATURE_MS2.AREA_INTENSITY of osw files.
`leftWidth` | (numeric) as in FEATURE.LEFT_WIDTH of osw files.
`rightWidth` | (numeric) as in FEATURE.RIGHT_WIDTH of osw files.
`peak_group_rank` | (integer) rank of each feature associated with transition_group_id.
`m_score` | (numeric) q-value of each feature associated with transition_group_id.
`chromatogramIndex` | (integer) Index of chromatogram in mzML file.
`transition_ids` | (integer) fragment-ion ID associated with transition_group_id. This is matched with chromatogram ID in mzML file.

### 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

`getRunNames`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    filenames <- getRunNames(dataPath = dataPath)
    ## Not run:
    mzPntrs <- getMZMLpointers(filenames)
    oswFiles <- getOswFiles(filenames, mzPntrs, analyteInGroupLabel = TRUE)
    rm(mzPntrs)

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]