makeTreeSEFromDADA2: Coerce 'DADA2' results to 'TreeSummarizedExperiment'

In microbiome/mia: Microbiome analysis

Coerce ‘DADA2’ results to TreeSummarizedExperiment

Description

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

Usage

makeTreeSEFromDADA2(...)

makeTreeSummarizedExperimentFromDADA2(...)

Arguments

...	See mergePairs function for more details.

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.

Value

An object of class TreeSummarizedExperiment

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
}

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.