inflateErr

(Required). A numeric matrix of transition rates (16 rows, named "A2A", "A2C", ...).

(Required). The fold-factor by which to inflate the transition rates.

inflation

(Optional). Default FALSE.
If True, self-transitions (eg. A->A) are also inflated.

inflateSelfTransitions


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


The dada2 package provides "OTU picking" functionality, but instead
of picking OTUs the DADA2 algorithm exactly infers samples sequences. The dada2
pipeline starts from demultiplexed fastq files, and outputs inferred sample
sequences and associated abundances after removing substitution and chimeric
errors. Taxonomic classification is also available via a native implementation
of the RDP classifier method.

Benjamin Callahan

dada2

Accurate, high-resolution sample inference from amplicon
sequencing data

inflateErr function

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)

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

Description

Usage

Arguments

Value

Examples