loessErrfun: Use a loess fit to estimate error rates from transition...

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

Use a loess fit to estimate error rates from transition counts.

Description

This function accepts a matrix of observed transitions, with each transition corresponding to a row (eg. row 2 = A->C) and each column to a quality score (eg. col 31 = Q30). It returns a matrix of estimated error rates of the same shape. Error rates are estimates by a loess fit of the observed rates of each transition as a function of the quality score. Self-transitions (i.e. A->A) are taken to be the left-over probability.

Usage

loessErrfun(trans)

Arguments

trans

(Required). A matrix of the observed transition counts. Must be 16 rows, with the rows named "A2A", "A2C", ...

Value

A numeric matrix with 16 rows and the same number of columns as trans. The estimated error rates for each transition (row, eg. "A2C") and quality score (column, eg. 31), as determined by loess smoothing over the quality scores within each transition category.

Examples

derep1 <- derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
dada1 <- dada(derep1, err=tperr1)
err.new <- loessErrfun(dada1$trans)

benjjneb/dada2 documentation built on Feb. 1, 2024, 10:50 p.m.