Description Usage Arguments Value See Also Examples
This function is a wrapper around isShift for collections of unique sequences. Each unique sequence is evaluated against a set of "parents" drawn from the sequence collection that are more abundant than the sequence being evaluated.
1 | isShiftDenovo(unqs, minOverlap = 20, flagSubseqs = FALSE, verbose = FALSE)
|
unqs |
(Required). A |
minOverlap |
(Optional). A |
flagSubseqs |
(Optional). A |
verbose |
(Optional). |
logical
of length the number of input unique sequences.
TRUE if sequence is an exact shift of a more abundant sequence. 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.shift <- isShiftDenovo(dada1)
is.shift <- isShiftDenovo(dada1$denoised, minOverlap=50, verbose=TRUE)
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