getFeature: Generate location features

Description Usage Arguments Value

View source: R/prepare.R

Description

Generate location features for each ATR event.

Usage

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getFeature(
  isoPLas,
  anno_event,
  depth.exon = 100,
  depth.intron = 300,
  cores = max(1, detectCores() - 2),
  remove.duplicate = TRUE,
  verbose = FALSE
)

Arguments

isoPLas

isoform parts list with AS events.

anno_event

DataFrame, event annotation w/o features.

depth.exon

integer, extended depth into exon, default 50 nt.

depth.intron

integer, extended depth into intron, default 300 nt.

cores

integer, number of computing cores to use.

remove.duplicate

logical, whether (default to TRUE) to remove identical event duplicates (by keeping one).

verbose

logical, whether (default to TRUE) to echo progress

Value

a surf object with one added column called feature, which contains a GRangesList of extracted location features.


fchen365/surf documentation built on June 18, 2021, 12:02 p.m.