Create a strollur object from dada2 outputs

This function reads a dada2 sequence table and creates a strollur::strollur object. The dada2 sequence table is a 2D matrix containing the abundance counts by sample for each ASV. The sample names are stored as row names and the sequence nucleotide strings are stored as column names.

To generate the dada2 sequence table from your own files you can follow this dada2 tutorial.

Usage

read_dada2(sequence_table, dataset_name = "")

Arguments

sequence_table

A dada2 sequence table

dataset_name

A string containing a name for your dataset.

Value

A strollur::strollur object

References

Callahan,B.J., McMurdie,P.J., Rosen,M.J., Han,A.W., Johnson,A.J.A. and Holmes,S.P. (2016), DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods 13:581-583. doi:10.1038/nmeth.3869

Examples

seqtab <- readRDS(strollur_example("dada2.rds"))
dim(seqtab)
#> [1]  19 279

data <- strollur::read_dada2(sequence_table = seqtab,
                               dataset_name = "dada2 example")
#> Added 279 sequences.
#> Assigned 279 sequence abundances.