Description Usage Arguments Value See Also Examples
This function is a wrapper around isBimera
for collections of unique
sequences (i.e. sequences with associated abundances). Each sequence is evaluated
against a set of "parents" drawn from the sequence collection that are sufficiently
more abundant than the sequence being evaluated. A logical vector is returned, with
an entry for each input sequence indicating whether it was (was not) consistent with
being a bimera of those more abundant "parents".
1 2 3 4 5 6 7 8 9 10 | isBimeraDenovo(
unqs,
minFoldParentOverAbundance = 2,
minParentAbundance = 8,
allowOneOff = FALSE,
minOneOffParentDistance = 4,
maxShift = 16,
multithread = FALSE,
verbose = FALSE
)
|
unqs |
(Required). A |
minFoldParentOverAbundance |
(Optional). A |
minParentAbundance |
(Optional). A |
allowOneOff |
(Optional). A |
minOneOffParentDistance |
(Optional). A |
maxShift |
(Optional). A |
multithread |
(Optional). Default is FALSE.
If TRUE, multithreading is enabled and the number of available threads is automatically determined.
If an integer is provided, the number of threads to use is set by passing the argument on to
|
verbose |
(Optional). |
logical
of length the number of input unique sequences.
TRUE if sequence is a bimera of more abundant "parent" sequences. Otherwise FALSE.
1 2 3 4 | derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
dada1 <- dada(derep1, err=tperr1, errorEstimationFunction=loessErrfun, selfConsist=TRUE)
is.bim <- isBimeraDenovo(dada1)
is.bim2 <- isBimeraDenovo(dada1$denoised, minFoldParentOverAbundance = 2, allowOneOff=TRUE)
|
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