findAdjacentFeature: Find adjacent features of given feature

Description Usage Arguments Value

View source: R/prepare.R

Description

Locate the adjacent bins at the desired direction and extract the genomic bins, given some location features of AS events. This is a helper function to getFeature().

Usage

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findAdjacentFeature(
  plas,
  body,
  type = c("lead", "lag"),
  depth.exon = 100,
  depth.intron = 300
)

Arguments

plas

one isoform element in isoPLas.

body

list, $id_tx, $event_id = body bins indices.

type

character, either"lead" for upstream, or "lag" for downstream.

depth.exon

integer, extended depth into exon, default 100 nt.

depth.intron

integer, extended depth into intron, default 300 nt.

Value

a GRangesList.


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