The read_biom function reads a biom formatted
file and creates a strollur::strollur object.
Examples
if (requireNamespace("h5lite", quietly = TRUE)) {
data <- strollur::read_biom(biom = strollur_example("miseq_sop.otu.biom"))
data
} else {
message(paste(
"To use this functionality you have to install the",
"h5lite package."
))
}
#> Added 531 sequences.
#> Assigned 531 sequence abundances.
#> Assigned 531 asv bins.
#> Assigned 531 asv bin taxonomies.
#> Added a report report.
#> miseq_sop:
#>
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 250 0 3 0 1.00
#> 2.5%-tile: 1 375 252 0 4 0 2850.05
#> 25%-tile: 1 375 252 0 4 0 28491.50
#> Median: 1 375 253 0 4 0 56982.00
#> 75%-tile: 1 375 253 0 5 0 85472.50
#> 97.5%-tile: 1 375 254 0 6 0 111113.95
#> Maximum: 1 375 256 0 6 0 113963.00
#> Mean: 1 375 252 0 4 0 56982.00
#>
#> Number of unique seqs: 531
#> Total number of seqs: 113963
#>
#> Total number of samples: 19
#> Total number of asvs: 531
#> Total number of asv bin classifications: 531
#> Total number of custom reports: 1
#>