pickNearestFeature: Pick feature closest to reference peak

Description Usage Arguments Value Author(s) See Also Examples

View source: R/post_alignment.R

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

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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, shubh.gupta@mail.utoronto.ca

ORCID: 0000-0003-3500-8152

License: (c) Author (2019) + GPL-3 Date: 2019-12-13

See Also

getFeatures

Examples

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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.