Create a TreeSummarizedExperiment object from ‘DADA2’ results

Create a TreeSummarizedExperiment object from ‘DADA2’ results

convertFromDADA2(...)

Arguments

...

Additional arguments. For convertFromDADA2, see mergePairs function for more details.

Value

convertFromDADA2 returns an object of class TreeSummarizedExperiment

Details

convertFromDADA2 is a wrapper for the mergePairs function from the dada2 package. A count matrix is constructed via makeSequenceTable(mergePairs(...)) and rownames are dynamically created as ASV(N) with N from 1 to nrow of the count tables. The colnames and rownames from the output of makeSequenceTable are stored as colnames and in the referenceSeq slot of the TreeSummarizedExperiment, respectively.

Examples

### Coerce DADA2 results to a TreeSE object
if(requireNamespace("dada2")) {
  fnF <- system.file("extdata", "sam1F.fastq.gz", package="dada2")
  fnR = system.file("extdata", "sam1R.fastq.gz", package="dada2")
  dadaF <- dada2::dada(fnF, selfConsist=TRUE)
  dadaR <- dada2::dada(fnR, selfConsist=TRUE)

  tse <- convertFromDADA2(dadaF, fnF, dadaR, fnR)
  tse
}
#> Loading required namespace: dada2
#> Initializing error rates to maximum possible estimate.
#> selfConsist step 1 .
#>    selfConsist step 2
#>    selfConsist step 3
#>    selfConsist step 4
#> Convergence after  4  rounds.
#> Initializing error rates to maximum possible estimate.
#> selfConsist step 1 .
#>    selfConsist step 2
#>    selfConsist step 3
#>    selfConsist step 4
#> Convergence after  4  rounds.
#> class: TreeSummarizedExperiment 
#> dim: 4 1 
#> metadata(0):
#> assays(1): counts
#> rownames(4): ASV01 ASV02 ASV03 ASV04
#> rowData names(0):
#> colnames: NULL
#> colData names(0):
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: NULL
#> rowTree: NULL
#> colLinks: NULL
#> colTree: NULL
#> referenceSeq: a DNAStringSet (4 sequences)