getFeatures {DIAlignR} | R Documentation

## Get features from all feature files

### Description

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

### Usage

    getFeatures(
      fileInfo,
      maxFdrQuery = 0.05,
      maxIPFFdrQuery = 0.05,
      runType = "DIA_Proteomics",
      applyFun = lapply
    )

### Arguments

`fileInfo` | (data-frame) output of `getRunNames` function.
`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".
`applyFun` | (function) value must be either lapply or BiocParallel::bplapply.

### Value

(list of dataframes) each dataframe 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. (If using 'DIA_IPF' runType, this will represent IPF's QVALUE)
`ms2_m_score` | (numeric) MS2 q-value of each feature associated with transition_group_id. (Will only be present if using 'DIA_IPF' runType)

### Author(s)

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

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-04-06

### See Also

`getRunNames, fetchPrecursorsInfo`

### Examples

    dataPath <- system.file("extdata", package = "DIAlignR")
    fileInfo <- getRunNames(dataPath = dataPath)
    features <- getFeatures(fileInfo, maxFdrQuery = 1.00, runType = "DIA_Proteomics")
    dim(features[[2]]) # 938  8

[Package DIAlignR version 2.2.0 Index]