get_orf_elong: Get the mean dwell time over all translated codons for a set...

In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

Get the mean dwell time over all translated codons for a set of transcripts

Description

Get the mean dwell time over all translated codons for a set of transcripts

Usage

get_orf_elong(anno, codon_model)

Arguments

anno	an annotation object
codon_model	a dwell-time data frame with columns position, codon, estimate

Details

Use estimates of per codon dwell time to get the mean dwell time

Value

a data frame with columns orf_id, mean_occ

Author(s)

Dermot Harnett, [e-mail]

Examples

data(chr22_anno)
data(rpfs)
data(offsets_df)
psites <- get_psite_gr(rpfs, offsets_df, chr22_anno)
rust_codon_occ_df <- get_codon_occs(psites, offsets_df, chr22_anno,
  n_genes = 1000, method = "RUST"
)
orf_elong <- get_orf_elong(chr22_anno, rust_codon_occ_df)
gn_elong <- gene_level_elong(orf_elong, ritpms, anno)

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