count_footprints: Count RPFs by position, frame, and length

In amandamok/choros: Bias Correction for Ribosome Profiling Data

Count RPFs by position, frame, and length

Description

This function aggregates RPF counts for a given transcript, codon position, and 5' and 3' digest lengths (which correspond to an RPF length and frame).

Usage

count_footprints(
  bam_dat,
  regression_data,
  which_column = "count",
  features = c("transcript", "cod_idx", "d5", "d3"),
  integer_counts = T
)

Arguments

bam_dat	data frame; output from 'load_bam'
regression_data	data frame; output from 'init_data'
which_column	character; name of column containing counts in 'bam_dat'
features	character vector; terms to match between 'regression_data' and 'bam_dat'
integer_counts	logical; whether to round counts to integers

Value

A numeric vector of RPF counts corresponding to rows in 'regression_data'

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