p_prior_errors: Computes prior probability of errors

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

Computes prior probability of errors

Description

This is an auxiliary function in single package. It takes a data frame with counts by position, nucleotide and Qscore and it summarises it into proportion of nucleotide counts by position.

Usage

p_prior_errors(counts_pnq, output_file = NULL, save = FALSE)

Arguments

counts_pnq	Data frame with columns position nucleoide quality counts, as returned by parse_countspnq
output_file	File name for output, if save=TRUE.
save	Logical. Should data be saved in a output_file?

Value

Data frame with columns position nucleotide prior.error.

Examples

refseq_fasta <- system.file("extdata", "ref_seq.fasta", package = "single")
train_reads_example <- system.file("extdata", "train_seqs_500.sorted.bam",
                                   package = "single")
counts_pnq <- pileup_by_QUAL(train_reads_example,pos_start=1,pos_end=10)
p_prior_errors <- p_prior_errors(counts_pnq=counts_pnq)
head(p_prior_errors)

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