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dada_denoise.Rd
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dada_denoise.Rd
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/rexmap.R
\name{dada_denoise}
\alias{dada_denoise}
\title{DADA2 denoising}
\usage{
dada_denoise(
fastq_trimmed,
fastq_untrimmed,
pvalue = 1e-04,
pvalue_adjusted = NULL,
multithread = rexmap_option("ncpu"),
verbose = rexmap_option("verbose"),
timing = rexmap_option("timing"),
dada_errors_path = NULL
)
}
\arguments{
\item{pvalue}{P-value threshold before Bonferroni correction for DADA2.}
\item{pvalue_adjusted}{P-value threshold after Bonferroni correction for DADA2.
If left as NULL, adjusted pvalue is calculated by taking \code{pvalue} and
dividing it by the maximum number of unique sequences across all samples.}
\item{multithread}{TRUE/FALSE or the number of CPU threads to use for multithreading.
Does not work on Windows due to \code{parallel} package implementation.}
\item{verbose}{TRUE/FALSE: display of status messages.}
\item{dada_errors_path}{Path to the Rdata object containing previously calcualted
DADA2 error matrix}
}
\description{
Uses DADA2 algorithm to denoise trimmed FASTQ files \code{fastq_trimmed}.
DADA2 partitions sequences based on their quality score profiles, using a
\code{pvalue_adjusted} parameter (\code{OMEGA_A} in the paper) as a cutoff
for forming new partitions. (See DADA2 paper
[Callahan et al. Nature Methods 2016] for details.)
If \code{pvalue}
is given (default), then the \code{pvalue_threshold} is calculated by dividing
the \code{pvalue} by the maximum number of unique sequences from all samples.
Otherwise \code{pvalue_threshold} is used directly.
}
\details{
After denoising, the untrimmed parts of sequences are retrieved from
\code{fastq_untrimmed} files and for each partition a consensus sequence
of that part is concatenaded to its end, omitting everything after
(and including) any indel and N.
}