getErrors: Extract already computed error rates.

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

Extract already computed error rates.

Description

Extract already computed error rates.

Usage

getErrors(obj, detailed = FALSE, enforce = TRUE)

Arguments

obj	(Required). An R object with error rates. Supported objects: dada-class; list of dada-class; numeric matrix; named list with $err_out, $err_in, $trans.
detailed	(Optional). Default FALSE. If FALSE, an error rate matrix corresponding to $err_out is returned. If TRUE, a named list with $err_out, $err_in and $trans. $err_in and $trans can be NULL.
enforce	(Optional). Default TRUE. If TRUE, will check validity of $err_out and error if invalid or NULL.

Value

A numeric matrix of error rates. Or, if detailed=TRUE, a named list with $err_out, $err_in and $trans.

Examples

 fl1 <- system.file("extdata", "sam1F.fastq.gz", package="dada2")
 drp <- derepFastq(fl1)
 dd <- dada(drp, err=NULL, selfConsist=TRUE)
 err <- getErrors(dd)

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.