dada2 (version 1.0.3)

removeBimeraDenovo: Remove bimeras from collections of unique sequences.

Description

This function is a wrapper around isBimeraDenovo. Bimeras identified by isBimeraDenovo are removed, and a bimera-free collection of unique sequences is returned.

Usage

removeBimeraDenovo(unqs, ..., verbose = FALSE)

Arguments

unqs

(Required). A uniques-vector or any object that can be coerced into one with getUniques. A list of such objects can also be provided.

...

(Optional). Arguments to be passed to isBimeraDenovo.

verbose

(Optional). logical(1) indicating verbose text output. Default FALSE.

Value

A uniques vector, or an object of matching class if a data.frame or sequence table is provided. A list of such objects is returned if a list of input unqs was provided.

See Also

isBimeraDenovo

Examples

derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
dada1 <- dada(derep1, err=tperr1, errorEstimationFunction=loessErrfun, selfConsist=TRUE)
out.nobim <- removeBimeraDenovo(dada1)
out.nobim <- removeBimeraDenovo(dada1$clustering, minFoldParentOverAbundance = 2, allowOneOff=FALSE)