add_rse {MultiDataSet} | R Documentation

## Method to add a `RangedSummarizedExperiment` to `MultiDataSet`.

### Description

This method adds or overwrites a slot of a `MultiDataSet` with the content of the given `RangedSummarizedExperiment`.

### Usage

    add_rse(object, set, dataset.type, dataset.name = NULL,
      sample.tables = NULL, feature.tables = NULL, warnings = TRUE,
      overwrite = FALSE)

### Arguments

`object` | `MultiDataSet` that will be filled.
`set` | Object derived from `RangedSummarizedExperiment` to be used to fill the slot.
`dataset.type` | Character with the type of data of the omic set (e.g. expression, methylation...)
`dataset.name` | Character with the specific name for this set (NULL by default). It is useful when there are several sets of the same type (e.g. multiple expression assays)
`sample.tables` | Character with the names of the slots with sample data besides colData.
`feature.tables` | Character with the names of the slots with feature data besides rowData.
`warnings` | Logical to indicate if warnings will be displayed.
`overwrite` | Logical to indicate if the set stored in the slot will be overwritten.

### Value

A new `MultiDataSet` with a slot filled.

### Examples

    if (require(GenomicRanges) & require(SummarizedExperiment)){
    multi <- createMultiDataSet()
    counts <- matrix(runif(200 * 6, 1, 1e4), 200)
    rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                         IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                         strand=sample(c("+", "-"), 200, TRUE),
                         feature_id=sprintf("ID%03d", 1:200))
    colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
                        row.names=LETTERS[1:6], id = LETTERS[1:6])
    names(rowRanges) <- 1:200
    rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
                                rowRanges=rowRanges, colData=colData)
    multi <- add_rse(multi, rse, "rseEx")
    }

[Package MultiDataSet version 1.14.0 Index]