get_cds_reads: Filter an RPF GR for overlap with coding sequences

get_cds_readsR Documentation

Filter an RPF GR for overlap with coding sequences

Description

Filter an RPF GR for overlap with coding sequences

Usage

get_cds_reads(cov, anno)

Arguments

cov

GRanges; A granges object with

anno

An annotation object

Details

This function reads in a bam file containing ribosomal footprints. It uses only reads without splice sites and reads which align to the positive strand, as it's designed to work on transcriptomic alignments.

Value

This function returns a granges object with the read names in the names slot and a metadata column denoting readlength.

Author(s)

Dermot Harnett, dermot.p.harnett@gmail.com

See Also

get_cds_reads, get_readlens


zslastman/RiboStan documentation built on June 12, 2024, 1:59 a.m.