convertFromDADA2: Create a 'TreeSummarizedExperiment' object from 'DADA2'...

In FelixErnst/mia: Microbiome analysis

Create a TreeSummarizedExperiment object from ‘DADA2’ results

Description

Create a TreeSummarizedExperiment object from ‘DADA2’ results

Usage

convertFromDADA2(...)

Arguments

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

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.

Value

convertFromDADA2 returns an object of class TreeSummarizedExperiment

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
}

FelixErnst/mia documentation built on Sept. 25, 2024, 8:55 p.m.