fetchFeaturesFromRun: Get features from a feature file.

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

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, [e-mail]

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)

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