makeTreeSummarizedExperimentFromDADA2 {mia}

R Documentation

Coerce ‘DADA2’ results to TreeSummarizedExperiment

Description

makeTreeSummarizedExperimentFromDADA2 is a wrapper for the mergePairs function from the dada2 package.

Usage

makeTreeSummarizedExperimentFromDADA2(...)

Arguments

...	See mergePairs function for more details.

Details

A count matrix is contructed 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.

Value

An object of class TreeSummarizedExperiment

See Also

makeTreeSummarizedExperimentFromPhyloseq makeSummarizedExperimentFromBiom loadFromQIIME2 loadFromMothur

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 <- makeTreeSummarizedExperimentFromDADA2(dadaF, fnF, dadaR, fnR)
  tse
}

---