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loadFrom* documentation
The function loadFromBiom
has outdated example section:
- refers to
se
(nottse
) as function output, although the function seems to return TreeSE - converts SE to TreeSE although the object is already SE before the conversion
Suggestion: fix this and check other functions for similar issue.
This is the problematic example:
if(requireNamespace("biomformat")) {
library(biomformat)
# load from file
rich_dense_file = system.file("extdata", "rich_dense_otu_table.biom",
package = "biomformat")
se <- loadFromBiom(rich_dense_file, removeTaxaPrefixes = TRUE)
# load from object
x1 <- biomformat::read_biom(rich_dense_file)
se <- makeTreeSEFromBiom(x1)
# Convert SE to TreeSE
tse <- as(se, "TreeSummarizedExperiment")
tse
}