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Import DADA2-style Outputs as a microbiome_dataset

Source: R/convert_microbiome_dataset.R
import_dada2.Rd

Import DADA2-style Outputs as a microbiome_dataset

Usage

import_dada2(
  seqtab,
  taxonomy_table = NULL,
  sample_info = NULL,
  taxa_are_rows = TRUE,
  otu_tree = NULL,
  taxa_tree = NULL,
  ref_seq = NULL,
  ...
)

Arguments

seqtab

A DADA2 sequence table with features in rows or columns.

taxonomy_table

Optional taxonomy table.

sample_info

Optional sample metadata table.

taxa_are_rows

Whether seqtab already has taxa in rows.

otu_tree

Optional OTU tree as phylo or treedata.

taxa_tree

Optional taxonomy tree as phylo or treedata.

ref_seq

Optional DNAStringSet.

...

Passed to create_microbiome_dataset().

Value

A microbiome_dataset object.

Examples

seqtab <- matrix(
  c(10, 0, 3, 8),
  nrow = 2,
  dimnames = list(c("ASV1", "ASV2"), c("Sample1", "Sample2"))
)
x <- import_dada2(seqtab = seqtab, taxa_are_rows = TRUE)
dim(x@expression_data)
#> [1] 2 2