makeSummarizedExperimentFromExpressionSet {SummarizedExperiment} | R Documentation

## Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versa

### Description

Coercion between RangedSummarizedExperiment and ExpressionSet is supported in both directions.

For going from ExpressionSet to RangedSummarizedExperiment, the `makeSummarizedExperimentFromExpressionSet` function is also provided to let the user control how to map features to ranges.

### Usage

    makeSummarizedExperimentFromExpressionSet(from,
                                              mapFun=naiveRangeMapper,
                                              ...)

    ## range mapping functions
    naiveRangeMapper(from)
    probeRangeMapper(from)
    geneRangeMapper(txDbPackage, key = "ENTREZID")

### Arguments

`from` | An ExpressionSet object.
`mapFun` | A function which takes an ExpressionSet object and returns a GRanges, or GRangesList object which corresponds to the genomic ranges used in the ExpressionSet. The rownames of the returned GRanges are used to match the featureNames of the ExpressionSet. The `naiveRangeMapper` function is used by default.
`...` | Additional arguments passed to `mapFun`.
`txDbPackage` | A character string with the Transcript Database to use for the mapping.
`key` | A character string with the Gene key to use for the mapping.

### Value

`makeSummarizedExperimentFromExpressionSet` takes an ExpressionSet object as input and a range mapping function that maps the features to ranges. It then returns a RangedSummarizedExperiment object that corresponds to the input.

The range mapping functions return a GRanges object, with the `rownames` corresponding to the featureNames of the ExpressionSet object.

### Author(s)

Jim Hester, james.f.hester@gmail.com

### See Also

- RangedSummarizedExperiment objects.

- ExpressionSet objects in the Biobase package.

- TxDb objects in the GenomicFeatures package.

### Examples

    ## ---------------------------------------------------------------------
    ## GOING FROM ExpressionSet TO SummarizedExperiment
    ## ---------------------------------------------------------------------

    data(sample.ExpressionSet, package="Biobase")

    # naive coercion
    makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)
    as(sample.ExpressionSet, "RangedSummarizedExperiment")
    as(sample.ExpressionSet, "SummarizedExperiment")

    # using probe range mapper
    makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)

    # using the gene range mapper
    se <- makeSummarizedExperimentFromExpressionSet(
        sample.ExpressionSet,
        geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene")
    )
    se
    rowData(se)  # duplicate row names

    ## ---------------------------------------------------------------------
    ## GOING FROM SummarizedExperiment TO ExpressionSet
    ## ---------------------------------------------------------------------

    example(RangedSummarizedExperiment)  # to create 'rse'
    rse
    as(rse, "ExpressionSet")

[Package SummarizedExperiment version 1.14.1 Index]