Description Usage Arguments Value See Also Examples
This function implements a table-specific version of de novo bimera detection. In short, bimeric sequences are flagged on a sample-by-sample basis. Then, a vote is performed for each sequence across all samples in which it appeared. If the sequence is flagged in a sufficiently high fraction of samples, it is identified as a bimera. A logical vector is returned, with an entry for each sequence in the table indicating whether it was identified as bimeric by this consensus procedure.
1 2 3 4 5 6 7 8 9 10 11 12 | isBimeraDenovoTable(
seqtab,
minSampleFraction = 0.9,
ignoreNNegatives = 1,
minFoldParentOverAbundance = 1.5,
minParentAbundance = 2,
allowOneOff = FALSE,
minOneOffParentDistance = 4,
maxShift = 16,
multithread = FALSE,
verbose = FALSE
)
|
seqtab |
(Required). A sequence table. That is, an integer matrix with colnames corresponding to DNA sequences. |
minSampleFraction |
(Optional). Default is 0.9. The fraction of samples in which a sequence must be flagged as bimeric in order for it to be classified as a bimera. |
ignoreNNegatives |
(Optional). Default is 1.
The number of unflagged samples to ignore when evaluating whether the fraction of samples
in which a sequence was flagged as a bimera exceeds |
minFoldParentOverAbundance |
(Optional). Default is 1.5. Only sequences greater than this-fold more abundant than a sequence can be its "parents". Evaluated on a per-sample basis. |
minParentAbundance |
(Optional). Default is 2. Only sequences at least this abundant can be "parents". Evaluated on a per-sample basis. |
allowOneOff |
(Optional). Default is FALSE. If FALSE, sequences that have one mismatch or indel to an exact bimera are also flagged as bimeric. |
minOneOffParentDistance |
(Optional). Default is 4. Only sequences with at least this many mismatches to the potential bimeric sequence considered as possible "parents" when flagging one-off bimeras. There is no such screen when considering exact bimeras. |
maxShift |
(Optional). Default is 16. Maximum shift allowed when aligning sequences to potential "parents". |
multithread |
(Optional). Default is FALSE. If TRUE, multithreading is enabled. NOT YET IMPLEMENTED. |
verbose |
(Optional). Default FALSE. Print verbose text output. |
logical
of length equal to the number of sequences in the input table.
TRUE if sequence is identified as a bimera. Otherwise FALSE.
1 2 3 4 5 6 | derep1 = derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
derep2 = derepFastq(system.file("extdata", "sam2F.fastq.gz", package="dada2"))
dd <- dada(list(derep1,derep2), err=NULL, errorEstimationFunction=loessErrfun, selfConsist=TRUE)
seqtab <- makeSequenceTable(dd)
isBimeraDenovoTable(seqtab)
isBimeraDenovoTable(seqtab, allowOneOff=TRUE, minSampleFraction=0.5)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.