getRefExpFeatureMap: Alignment Feature Mapping Table

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

Alignment Feature Mapping Table

Description

Construct an alignment feature mapping table for star align method, to map aligned features in experiment runs to the reference run

Usage

getRefExpFeatureMap(precursors, features, applyFun = lapply)

Arguments

precursors	(data-frames) Contains precursors and associated transition IDs.
features	(list of data-frames) Contains features and their properties identified in each run.
applyFun	(function) value must be either lapply or BiocParallel::bplapply.

Value

(list) of dataframes per precursor peptide id having following columns:

reference_feature_id	(integer) id of reference feature.
experiment_feature_id	(integer) id of experiment feature aligned to reference feature.

Author(s)

Justin Sing, [e-mail]

ORCID: 0000-0003-0386-0092

License: (c) Author (2020) + GPL-3 Date: 2022-11-07

See Also

getPrecursors, getFeatures

Examples

dataPath <- system.file("extdata", package = "DIAlignR")
fileInfo <- getRunNames(dataPath, oswMerged = TRUE)
precursors <- getPrecursors(fileInfo, oswMerged = TRUE, context = "experiment-wide")
features <- getFeatures(fileInfo, maxFdrQuery = 0.05)
multiFeatureAlignmentMap <- getRefExpFeatureMap(precursors, features)
multiFeatureAlignmentMap[["9861"]]

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