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
    }

[Package mia version 1.2.7 Index]