Coerce ‘DADA2’ results to TreeSummarizedExperiment

makeTreeSEFromDADA2 is a wrapper for the mergePairs function from the dada2 package.

makeTreeSEFromDADA2(...)

makeTreeSummarizedExperimentFromDADA2(...)

Arguments

...

See mergePairs function for more details.

Value

An object of class TreeSummarizedExperiment

Details

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.

See also

makeTreeSEFromPhyloseq makeTreeSEFromBiom importQIIME2 importMothur

Examples

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 <- makeTreeSEFromDADA2(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)