dot-getCDSRegions: Get CDS start and end regions

In nzhang89/RiboSeeker: A Package for Ribosome Profiling Data Analysis and Visualization

Get CDS start and end regions

Description

Get CDS start and end regions

Usage

.getCDSRegions(
  txdb,
  seqInfoKeep,
  cdsStartUpstream,
  cdsStartDownstream,
  cdsEndUpstream,
  cdsEndDownstream
)

Arguments

txdb	A TxDb object of genome annotation. See GenomicFeatures package for more details.
seqInfoKeep	A Seqinfo object specifying which seqlevels in txdb to keep.
cdsStartUpstream	A numeric variable indicating the width to use for the upstream region of CDS start site (not including CDS start site).
cdsStartDownstream	A numeric variable indicating the width to use for the downstream region of CDS start site (including CDS start site).
cdsEndUpstream	A numeric variable indicating the width to use for the upstream region of CDS end site (including CDS end site).
cdsEndDownstream	A numeric variable indicating the width to use for the downstream region of CDS end site (not including CDS end site).

Value

a list of 3 elements, CDS start region, CDS end region, and transcript id (names of the list are "start", "end", and "tx"). CDS start and end regions are both GRanges objects with a mcol of "tx".

nzhang89/RiboSeeker documentation built on April 15, 2022, 10:18 a.m.