pickNearestFeature: Pick feature closest to reference peak

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

Description

It picks a feature that is within adaptiveRT window across eXpRT and has lowest m-score. Feature's m-score also has to be smaller than featureFDR.

Usage

pickNearestFeature(eXpRT, analyte, oswFiles, runname, adaptiveRT, featureFDR)

Arguments

eXpRT	(numeric) retention time in experiment run.
analyte	(integer) vector of precursor IDs.
oswFiles	(list of data-frames) it is output from getFeatures function.
runname	(string) must be a combination of "run" and an iteger e.g. "run2".
adaptiveRT	(numeric) half-width of retention time window. Feature, if found, is picked from within this window.
featureFDR	(numeric) upper m-score cut-off for a feature to be picked.

Value

(list) Following elements are present in the list:

leftWidth	(numeric) as in FEATURE.LEFT_WIDTH of osw files.
rightWidth	(numeric) as in FEATURE.RIGHT_WIDTH of osw files.
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.
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: 2019-12-13

See Also

getFeatures

Examples

data(oswFiles_DIAlignR, package="DIAlignR")
## Not run: 
pickNearestFeature(eXpRT = 5237.8, analyte = 4618L, oswFiles = oswFiles_DIAlignR,
 runname = "run2", adaptiveRT = 77.82315, featureFDR = 0.05)

## End(Not run)

Roestlab/DIAlign documentation built on Feb. 25, 2021, 5:18 p.m.