getFeatures: Get features from all feature files

getFeaturesR 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

shubham1637/DIAlign documentation built on March 27, 2023, 7:12 a.m.