fetchAnalytesInfo {DIAlignR} | R Documentation

## Fetch features of analytes

### Description

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

### Usage

    fetchAnalytesInfo(
      oswName,
      maxFdrQuery,
      oswMerged,
      analytes,
      filename,
      runType,
      analyteInGroupLabel = FALSE
    )

### Arguments

`oswName` | (char) path to the 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.
`oswMerged` | (logical) TRUE for experiment-wide FDR and FALSE for run-specific FDR by pyprophet.
`analytes` | (vector of strings) transition_group_ids for which features are to be extracted. analyteInGroupLabel must be set according the pattern used here.
`filename` | (data-frame) Should be from the RUN.FILENAME column from osw files.
`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. FALSE for fetching analytes as PEPTIDE.MODIFIED_SEQUENCE and PRECURSOR.CHARGE from osw file.

### 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.
`filename` | (string) as mentioned in RUN table of osw files.
`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.
`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 <- DIAlignR::getRunNames(dataPath = dataPath)
    oswName <- paste0(dataPath,"/osw/merged.osw")
    ## Not run:
    analytesInfo <- fetchAnalytesInfo(oswName, maxFdrQuery = 0.05, oswMerged = TRUE,
     analytes = c("19051_KLIVTSEGC[160]FK/2"), filename = filenames$filename[2],
      runType = "DIA_proteomics", analyteInGroupLabel = TRUE)
    analytesInfo <- fetchAnalytesInfo(oswName, maxFdrQuery = 0.05, oswMerged = TRUE,
     analytes = c("IHFLSPVRPFTLTPGDEEESFIQLITPVR_3"), filename = filenames$filename[3],
      runType = "DIA_proteomics", analyteInGroupLabel = FALSE)

    ## End(Not run)

[Package DIAlignR version 1.2.0 Index]