removeBimeraDenovo: Remove bimeras from collections of unique sequences.

Description Usage Arguments Value See Also Examples

View source: R/chimeras.R

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

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removeBimeraDenovo(unqs, method = "consensus", tableMethod = NULL, ...,
  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).

tableMethod

(DEPRECATED).

...

(Optional). Arguments to be passed to isBimeraDenovo or isBimeraDenovoTable.

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

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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, allowOneOff=FALSE)

Bioconductor-mirror/dada2 documentation built on June 1, 2017, 7:31 a.m.