fetchFeaturesFromRun: Get features from a feature file.
In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description Usage Arguments Value Author(s) See Also Examples

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

fetchFeaturesFromRun(
  filename,
  runID,
  maxFdrQuery = 1,
  runType = "DIA_proteomics"
)

`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".

(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.

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

ORCID: 0000-0003-3500-8152

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

getRunNames, getFeatures, getFeaturesQuery

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- DIAlignR::getRunNames(dataPath = dataPath)
## Not run: 
featuresInfo <- fetchFeaturesFromRun(fileInfo$featureFile[1], fileInfo$spectraFileID[1],
 maxFdrQuery = 0.05)
dim(featuresInfo) # 211  7

## End(Not run)