get_psite_gr: convert a granges object of footprints to a psites object

get_psite_grR Documentation

convert a granges object of footprints to a psites object

Description

This function applies offsets to RPF data, attributing to each RPF an offset specific a readlength and phase. Where phase is ambigous, because more than one ORF overlaps the RPF, the RPF has both offsets applied, and in rare cases where more than one possible psite location applies, one is randomly selected.

Usage

get_psite_gr(rpfs, offsets_df, anno)

Arguments

rpfs
  • granges object with positions of footprints, in transcript space

offsets_df
  • a data frame with numeric columns readlen,phase,offset

anno
  • an annotation object with at least one ORF per transcript, the function uses the 'uORF' slot if it's available

Value

a GRanges object of width-1 psites with columns readlen, phase and offset

Author(s)

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

Examples

data(chr22_anno)
data(rpfs)
data(offsets_df)
psites <- get_psite_gr(rpfs, offsets_df, anno)

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