calculate_codon_density: Calculate codon density

In amandamok/choros: Bias Correction for Ribosome Profiling Data

Calculate codon density

Description

This function returns a vector of RPF counts per codon for an individual transcrips.

Usage

calculate_codon_density(
  bam_dat,
  transcript_length,
  exclude_codons5 = 10,
  exclude_codons3 = 10,
  normalize = F,
  which_column = "count"
)

Arguments

bam_dat	data frame; output from 'load_bam'
transcript_length	integer; length of transcript CDS in codons
exclude_codons5	integer; number of codons to exclude from 5' end of transcript
exclude_codons3	integer; number of codons to exclude from 3' end of transcript
normalize	logical; whether to normalize codon counts by the average RPF count across the transcript
which_column	character; column in 'bam_dat' corresponding to RPF count

Value

A numeric vector of RPF counts per codon position

amandamok/choros documentation built on March 15, 2023, 7:57 p.m.