getFeatures: Get features from all feature files

In DIAlignR: Dynamic Programming Based Alignment of MS2 Chromatograms

Description

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

Usage

getFeatures(fileInfo, maxFdrQuery = 0.05, runType = "DIA_proteomics")

Arguments

fileInfo	(data-frame) Output of DIAlignR::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.
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	(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: 2019-04-06

See Also

getRunNames, fetchPrecursorsInfo

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- DIAlignR::getRunNames(dataPath = dataPath)
## Not run: 
features <- getFeatures(fileInfo, maxFdrQuery = 1.00, runType = "DIA_proteomics")
dim(features[[2]]) # 227  7

## End(Not run)

DIAlignR documentation built on Nov. 8, 2020, 8:22 p.m.