fetchTransitionsFromRun: Get transitions from a feature file

fetchTransitionsFromRunR Documentation

Get transitions from a feature file

Description

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

Usage

fetchTransitionsFromRun(
  filename,
  runID,
  maxFdrQuery = 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.

runType

(char) This must be one of the strings "DIA_Proteomics", "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

(list) of peak intensities as in FEATURE_TRANSITION.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 (2020) + GPL-3 Date: 2020-11-15

See Also

getRunNames, getTransitions, getTransitionsQuery

Examples

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

## End(Not run)

shubham1637/DIAlignR documentation built on March 29, 2023, 8:45 p.m.