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
    }

[Package mia version 1.2.7 Index]