init_data: Generate data frame to fit negative binomial regression model
In amandamok/choros: Bias Correction for Ribosome Profiling Data

init_data

R Documentation

Generate data frame to fit negative binomial regression model

Description

This function enumerates data points to train a regression model of RPF counts, given a list of transcripts for training

Usage

init_data(
  transcript_fa_fname,
  transcript_length_fname,
  digest5_lengths = 15:18,
  digest3_lengths = 9:11,
  d5_d3_subsets = NULL,
  f5_length = 3,
  f3_length = 3,
  num_cores = NULL,
  which_transcripts = NULL,
  exclude_codons5 = 10,
  exclude_codons3 = 10,
  compute_gc = T,
  gc_omit = "APE"
)

Arguments

`transcript_fa_fname`	character; file path to transcriptome .fasta file
`transcript_length_fname`	character; file path to transcriptome lengths file
`digest5_lengths`	integer vector; legal 5' digest lengths
`digest3_lengths`	integer vector; legal 3' digest lengths
`d5_d3_subsets`	data frame; columns of 'd5' and 'd3' to initiate data over
`f5_length`	integer; length of 5' bias sequence
`f3_length`	integer; length of 3' bias sequence
`num_cores`	integer; number of cores to use for parallelization
`which_transcripts`	character vector; transcripts selected for regression
`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
`compute_gc`	logical; whether to return RPF GC-content
`gc_omit`	character; one of 'A', 'AP', or 'APE' codons to omit for GC-content calculation