dadaMulti

A wrapper around dada of the dada2 packager for multiple amplicons.

dadaMulti(
  MA,
  mc.cores = getOption("mc.cores", 1L),
  Ferr = NULL,
  Rerr = NULL,
  ...
)

Arguments

MA	MultiAmplicon-class object.
mc.cores	mc.cores number or compute cores for parallel denoising of different amplicons (values > 1 are only allowed on Unix/Linux systems). Also consider parallelization at the level of each individual amplicon via dada.
Ferr	As in the "err" parameter of dada: the matrix of estimated rates for each possible nucleotide change. In this case for forward reads.
Rerr	the same for the reverse reads.
...	additional parameters to be passed to the dada function of dada2. All arguments to dadaMulti can be given as a vector of the same length as the number of primer pairs in the MultiAmplicon object. This allows to specify different parameters for each amplicon. If a shorter vector is given it will be recycled to match the number of amplicons.

Value

MultiAmplicon object with dadaF and dadaR slots filled.

Details

The function runs dada from the package dada2 to perform 'High resolution sample inference from amplicon data' on multiple amplicons stored as dereplicated sequences in a MultiAmplicon-class object.

Author

Emanuel Heitlinger