fetchTransitionsFromRun: Get transitions from a feature file

In shubham1637/DIAlign: Dynamic Programming Based Alignment of MS2 Chromatograms

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, [e-mail]

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