evaluate_fits: Evaluate SINGLE fits

In rocioespci/single: Accurate consensus sequence from nanopore reads of a gene library

Evaluate SINGLE fits

Description

Evaluates SINGLe for pos, nucleotides and QUAL in the given ranges.

Usage

evaluate_fits(
  pos_range,
  q_range,
  output_file,
  data_fits,
  ref_seq,
  verbose = FALSE,
  save = FALSE
)

Arguments

pos_range	Numeric vector. Positions to evaluate.
q_range	Numeric vector. QUAL to evaluate.
output_file	File name for output, if save=TRUE.
data_fits	Data.frame with columns position nucleotide slope intercept as the one returned by fit_logregr
ref_seq	DNAStringSet containing the true reference sequence.
verbose	Logical.
save	Logical. Should results be saved in output_file?

Value

data.frame with SINGLE fits evaluated for pos_range and q_range.

Examples

refseq_fasta = system.file("extdata", "ref_seq.fasta", package = "single")
ref_seq = Biostrings::readDNAStringSet(refseq_fasta)
fits_file <- system.file("extdata","fits_example.txt",package = "single")
fits <- read.table(fits_file, header=TRUE)
evaluated_fits <- evaluate_fits(pos_range = c(1,5),q_range = c(0,10),
                     data_fits = fits,ref_seq = ref_seq)

rocioespci/single documentation built on April 18, 2023, 8:48 p.m.