choros: Pipeline for RPF bias correction

In amandamok/choros: Bias Correction for Ribosome Profiling Data

Pipeline for RPF bias correction

Description

This is a wrapper function to perform all the steps in the 'choros' pipeline: pre-processing of the RPF alignments, deciding which RPF lengths and frames to model, deciding which transcripts to use for training, regression modeling, correction of RPF counts, and evaluation of position-based biases before/after correction.

Usage

choros(
  bam_fname,
  transcript_fa_fname,
  transcript_length_fname,
  offsets_fname,
  expt_dir = ".",
  save_intermediate = T,
  extra_args = NULL
)

Arguments

bam_fname	character; file path to .bam alignment file
transcript_fa_fname	character; file path to transcriptome .fasta file
transcript_length_fname	character; file path to transcriptome lengths file
offsets_fname	character; file path to offset / A site assignment rules .txt file
expt_dir	character; file path to directory to save output/intermediate files
save_intermediate	logical; whether to save intermediate files (if FALSE, only save alignment file with corrected weights)
extra_args	named list; additional parameters to pass onto internal functions

Value

A list containing: data frame of all RPF alignments with bias- corrected counts; data frame used for training the regression model; regression coefficients from the model fit; and a list of generated plots (diagnostic plot of RPF lengths and frames; bias evaluation per-codon and per-nucleotide position before and after bias correction)

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