inflateErr: Inflates an error rate matrix by a specified factor, while...

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

Inflates an error rate matrix by a specified factor, while accounting for saturation.

Description

Error rates are "inflated" by the specified factor, while appropriately saturating so that rates cannot exceed 1. The formula is: new_err_rate <- err_rate * inflate / (1 + (inflate-1) * err_rate)

Usage

inflateErr(err, inflation, inflateSelfTransitions = FALSE)

Arguments

err	(Required). A numeric matrix of transition rates (16 rows, named "A2A", "A2C", ...).
inflation	(Required). The fold-factor by which to inflate the transition rates.
inflateSelfTransitions	(Optional). Default FALSE. If True, self-transitions (eg. A->A) are also inflated.

Value

An error rate matrix of the same dimensions as the input error rate matrix.

Examples

 tperr2 <- inflateErr(tperr1, 2)
 tperr3.all <- inflateErr(tperr1, 3, inflateSelfTransitions=TRUE)

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