makeSummarizedExperimentFromBiom {mia} | R Documentation |
For convenience a few functions are available to convert data from a
‘biom’ file or object into a
SummarizedExperiment
loadFromBiom(file) makeSummarizedExperimentFromBiom(obj)
file |
biom file location |
obj |
object of type |
An object of class
SummarizedExperiment
makeTreeSummarizedExperimentFromphyloseq
makeTreeSummarizedExperimentFromDADA2
loadFromQIIME2
loadFromMothur
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) # load from object x1 <- biomformat::read_biom(rich_dense_file) se <- makeSummarizedExperimentFromBiom(x1) se }