getOswAnalytes {DIAlignR} | R Documentation

## Fetch analytes from OSW file

### Description

Get a data-frame of analytes, their chromatogram indices and associated FDR-scores.

### Usage

    getOswAnalytes(
      fileInfo,
      oswMerged = TRUE,
      analyteInGroupLabel = FALSE,
      maxFdrQuery = 0.05,
      runType = "DIA_proteomics"
    )

### Arguments

`oswMerged` | (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`analyteInGroupLabel` | (logical) TRUE for getting analytes as PRECURSOR.GROUP_LABEL from osw file. 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.
`runType` | (char) This must be one of the strings "DIA_proteomics", "DIA_Metabolomics".
`dataPath` | (char) path to mzml 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

(A list of data-frames) Each 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.
`filename` | (string) as mentioned in RUN table 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.
`transition_id` | (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:
    oswFiles <- getOswAnalytes(dataPath = dataPath, filenames = filenames,
     analyteInGroupLabel = TRUE)
    oswFiles[["run0"]][1,]
    oswFiles <- getOswAnalytes(dataPath = dataPath, filenames = filenames,
     analyteInGroupLabel = FALSE)
    oswFiles[["run0"]][1,]

    ## End(Not run)

[Package DIAlignR version 1.2.0 Index]