removeBimeraDenovo: Remove bimeras from collections of unique sequences.

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

Remove bimeras from collections of unique sequences.

Description

This function is a convenience interface for chimera removal. Two methods to identify chimeras are supported: Identification from pooled sequences (see isBimeraDenovo for details) and identification by consensus across samples (see isBimeraDenovoTable for details). Sequence variants identified as bimeric are removed, and a bimera-free collection of unique sequences is returned.

Usage

removeBimeraDenovo(unqs, method = "consensus", ..., 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.
method	(Optional). Default is "consensus". Only has an effect if a sequence table is provided. If "pooled": The samples in the sequence table are all pooled together for bimera identification (isBimeraDenovo). If "consensus": The samples in a sequence table are independently checked for bimeras, and a consensus decision on each sequence variant is made (isBimeraDenovoTable). If "per-sample": The samples in a sequence table are independently checked for bimeras, and sequence variants are removed (zeroed-out) from samples independently (isBimeraDenovo).
...	(Optional). Arguments to be passed to isBimeraDenovo or isBimeraDenovoTable. The documentation of those methods detail the additional algorithmic parameters that can be adjusted.
verbose	(Optional). Default FALSE. Print verbose text output.

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

isBimeraDenovoTable, 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, method="pooled", minFoldParentOverAbundance = 2)

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.