init_data: Generate data frame to fit negative binomial regression model

View source: R/prep_data.R

init_dataR 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

Value

data frame of data to use for downstream regression modeling


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