fetchFeaturesFromRun {DIAlignR} | R Documentation

## Get features from a feature file.

### Description

Get a data-frame of OpenSwath features that contains retention time, intensities, boundaries etc.

### Usage

    fetchFeaturesFromRun(
      filename,
      runID,
      maxFdrQuery = 1,
      maxIPFFdrQuery = 1,
      runType = "DIA_Proteomics"
    )

### Arguments

`filename` | (string) Path to the feature file.
`runID` | (string) id in RUN.ID column of the feature 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.
`maxIPFFdrQuery` | (numeric) A numeric value between 0 and 1. It is used to filter features from osw file which have SCORE_IPF.QVALUE less than itself. (For PTM IPF use)
`runType` | (char) This must be one of the strings "DIA_Proteomics", "DIA_IPF", "DIA_Metabolomics".

### Value

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

`transition_group_id` | (integer) a unique id for each precursor.
`RT` | (numeric) retention time as in FEATURE.EXP_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.

### Author(s)

Shubham Gupta, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-04-04

### See Also

`getRunNames, getFeatures, getFeaturesQuery`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    fileInfo <- getRunNames(dataPath = dataPath)
    ## Not run:
    featuresInfo <- fetchFeaturesFromRun(fileInfo$featureFile[1], fileInfo$spectraFileID[1],
     maxFdrQuery = 0.05)
    dim(featuresInfo) # 211  8

    ## End(Not run)

[Package DIAlignR version 2.2.0 Index]