get_codon_occs: Estimate per codon occupancies

In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

Estimate per codon occupancies

Description

Uses sampled RPF coverage gr object, offsets data frame, and an annotation object to get estimates of per-codon occupancy (which are proportional to dwell times)

Usage

get_codon_occs(
  psites,
  offsets_df,
  anno,
  n_genes = 1000,
  covthresh = 10,
  method = "linear"
)

Arguments

psites	a data frame of inferred RPF p-sites
offsets_df	a data frame with numeric columns readlen,phase,offset
anno	an annotation object
n_genes	how many genes to use for the model - most highly expressed used first
covthresh	how many reads to require in an ORF for it to be used defaults to RUST
method	which method to use to estimate the codon occupancies,

Value

a data frame with columns codon,position,estimate,upper,lower, p.value

Author(s)

Dermot Harnett, [e-mail]

Examples

data(chr22_anno)
data(rpfs)
data(offsets_df)
fafile <- here::here('chr22.fa')
library(BSgenome.Hsapiens.UCSC.hg38)
if(!file.exists(fafile)){
    seq <- Biostrings::DNAStringSet(BSgenome.Hsapiens.UCSC.hg38[['chr22']])
    names(seq) <- 'chr22'
    Biostrings::writeXStringSet(
    seq, fafile)}
Rsamtools::indexFa(fafile)
psites <- get_psite_gr(rpfs, offsets_df, chr22_anno)
rust_codon_occ_df <- get_codon_occs(psites, offsets_df, chr22_anno,
  n_genes = 200, method = "RUST"
)

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