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

In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

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, [e-mail]

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.