makeTreeSummarizedExperimentFromDADA2 {mia} | R Documentation |
TreeSummarizedExperiment
makeTreeSummarizedExperimentFromDADA2
is a wrapper for the
mergePairs
function from the dada2
package.
makeTreeSummarizedExperimentFromDADA2(...)
... |
See |
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.
An object of class TreeSummarizedExperiment
makeTreeSummarizedExperimentFromPhyloseq
makeSummarizedExperimentFromBiom
loadFromQIIME2
loadFromMothur
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 }