makeSummarizedExperimentFromBiom {mia}

R Documentation

Loading a biom file

Description

For convenience a few functions are available to convert data from a ‘biom’ file or object into a SummarizedExperiment

Usage

loadFromBiom(file)

makeSummarizedExperimentFromBiom(obj)

Arguments

file	biom file location
obj	object of type biom

Value

An object of class SummarizedExperiment

See Also

makeTreeSummarizedExperimentFromPhyloseq makeTreeSummarizedExperimentFromDADA2 loadFromQIIME2 loadFromMothur

Examples

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
}

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