compute_rpf_gc: Compute GC-content for a ribosome-protected fragment

In amandamok/choros: Bias Correction for Ribosome Profiling Data

Compute GC-content for a ribosome-protected fragment

Description

This function computes the GC-content of a ribosome-protected fragment, omitting the nucleotides in the A-, P-, and/or E-site codon positions.

Usage

compute_rpf_gc(
  dat,
  omit = "APE",
  transcript_fa_fname,
  transcript_lengths_fname,
  read_type = "monosome"
)

Arguments

dat	data frame containing columns 'transcript', 'cod_idx', 'd5', and 'd3'
omit	character; one of 'A', 'AP', or 'APE' corresponding to codons to omit
transcript_fa_fname	character; file path to transcriptome fasta file
transcript_lengths_fname	character; file path to transcript lengths file
read_type	character; one of 'monosome' or 'disome'

Value

A numeric vector corresponding to rows of 'dat'

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