gene_level_expr: Aggregate transcript level RiboPMs to the gene-level Ignores...

In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

Aggregate transcript level RiboPMs to the gene-level Ignores uORF expression

Description

Aggregate transcript level RiboPMs to the gene-level Ignores uORF expression

Usage

gene_level_expr(ripms, anno)

Arguments

ripms	named vector of ribosome densities
anno	An annotation object with a gene-transcript table

Details

This function reads in a vector of transcript-level ribosome footprint densitiies and aggregates values from transcripts of the same gene and outputs gene-level values

Value

a data frame with columns gene_id, expr

Author(s)

Dermot Harnett, [e-mail]

Examples

data(chr22_anno)
data(rpfs)
data(offsets_df)
data(ms_df)

psites <- get_psite_gr(rpfs, offsets_df, chr22_anno)
# now, use Stan to estimate normalized p-site densities for our data
ritpms <- get_ritpms(psites, chr22_anno)
# and get these at the gene level (ignoring uORFs)
gritpms <- gene_level_expr(ritpms, chr22_anno)

zslastman/RiboStan documentation built on April 6, 2024, 1:35 p.m.