calculate_transcript_density: Calculate per-transcript RPF density

In amandamok/choros: Bias Correction for Ribosome Profiling Data

Calculate per-transcript RPF density

Description

This function computes the mean or median footprint density per codon across all transcripts.

Usage

calculate_transcript_density(
  bam_dat,
  transcript_length_fname,
  statistic = mean,
  exclude_codons5 = 10,
  exclude_codons3 = 10
)

Arguments

bam_dat	data frame; output from 'load_bam'
transcript_length_fname	character; file path to transcriptome lengths file
statistic	character; one of 'mean' or 'median'
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

Value

A numeric vector of RPF density per transcript

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