dada2: isBimeraDenovoTable – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

isBimeraDenovoTable

Identify bimeras in a sequence table.

Description

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.

Usage

isBimeraDenovoTable(
  seqtab,
  minSampleFraction = 0.9,
  ignoreNNegatives = 1,
  minFoldParentOverAbundance = 1.5,
  minParentAbundance = 2,
  allowOneOff = FALSE,
  minOneOffParentDistance = 4,
  maxShift = 16,
  multithread = FALSE,
  verbose = FALSE
)

Arguments

`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 `minSampleFraction`. The purpose of this parameter is to lower the threshold at which sequences found in few samples are flagged as bimeras.
`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.

Value

logical of length equal to the number of sequences in the input table. TRUE if sequence is identified as a bimera. Otherwise FALSE.

Examples

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)

dada2

Accurate, high-resolution sample inference from amplicon sequencing data

v1.18.0

LGPL-3

Authors

Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes

Initial release

2020-08-07