MultiDataSet-class {MultiDataSet} | R Documentation

## MultiDataSet instances

### Description

The class `MultiDataSet` is a superior class to store multiple datasets in form of triplets (assayData-phenoData-featureData). The datasets can be `eSet` or `SummarizedExperiment` derived or `matrices`.

### Usage

    ## S4 method for signature 'MultiDataSet,eSet'
    add_eset(object, set, dataset.type,
      dataset.name = NULL, sample.tables = "protocolData",
      feature.tables = NULL, warnings = TRUE, overwrite = FALSE, GRanges)

    ## S4 method for signature 'MultiDataSet,ExpressionSet'
    add_genexp(object, gexpSet, ...)

    ## S4 method for signature 'MultiDataSet,ExpressionSet'
    add_rnaseq(object, rnaSet, ...)

    ## S4 method for signature 'MultiDataSet,GenomicRatioSet'
    add_methy(object, methySet, ...)

    ## S4 method for signature 'MultiDataSet,RangedSummarizedExperiment'
    add_rse(object, set,
      dataset.type, dataset.name = NULL, sample.tables = NULL,
      feature.tables = "elementMetadata", warnings = TRUE, overwrite = FALSE)

    ## S4 method for signature 'MultiDataSet,SummarizedExperiment'
    add_se(object, set, dataset.type,
      dataset.name = NULL, sample.tables = NULL,
      feature.tables = "elementMetadata", warnings = TRUE, overwrite = FALSE,
      GRanges)

    ## S4 method for signature 'MultiDataSet,SnpSet'
    add_snps(object, snpSet, ...)

    ## S4 method for signature 'MultiDataSet,matrix'
    add_table(object, set, dataset.type,
      dataset.name = NULL, warnings = TRUE, overwrite = FALSE)

    ## S4 method for signature 'MultiDataSet'
    as.list(x)

    ## S4 method for signature 'MultiDataSet'
    commonIds(object)

    ## S4 method for signature 'MultiDataSet'
    commonSamples(object, unify.names = FALSE)

    createMultiDataSet()

    ## S4 method for signature 'MultiDataSet'
    dims(x)

    ## S4 method for signature 'MultiDataSet'
    w_iclusterplus(object, commonSamples = TRUE, ...)

    ## S4 method for signature 'MultiDataSet'
    length(x)

    ## S4 method for signature 'MultiDataSet'
    w_mcia(object, ...)

    ## S4 method for signature 'MultiDataSet'
    names(x)

    ## S4 method for signature 'MultiDataSet'
    ncol(x)

    ## S4 method for signature 'MultiDataSet'
    nrow(x)

    ## S4 method for signature 'MultiDataSet'
    rowRangesElements(object)

    ## S4 method for signature 'MultiDataSet'
    sampleNames(object)

    ## S4 method for signature 'MultiDataSet'
    assayData(object)

    ## S4 method for signature 'MultiDataSet'
    fData(object)

    ## S4 method for signature 'MultiDataSet'
    featureData(object)

    ## S4 method for signature 'MultiDataSet'
    pData(object)

    ## S4 method for signature 'MultiDataSet'
    phenoData(object)

    ## S4 method for signature 'MultiDataSet'
    rowRanges(x)

    ## S4 method for signature 'MultiDataSet,ANY,ANY'
    x[[i]]

    ## S4 method for signature 'MultiDataSet,ANY,ANY,ANY'
    x[i, j, k, ..., drop = FALSE]

    ## S4 method for signature 'MultiDataSet'
    subset(x, feat, phe, warnings = TRUE, keep = TRUE)

### Arguments

`object` | `MultiDataSet`
`set` | Object derived from `eSet` 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
`sample.tables` | Character with the names of the slots with sample data besides phenoData.
`feature.tables` | Character with the names of the slots with feature data besides featureData.
`warnings` | Logical to indicate if warnings will be displayed.
`overwrite` | Logical to indicate if the set stored in the slot will be overwritten.
`GRanges` | `GenomicRanges` to be included in rowRanges slot.
`gexpSet` | `ExpressionSet` to be used to fill the slot.
`...` | Further arguments passed to add_rse or add_se
`rnaSet` | `ExpressionSet` to be used to fill the slot.
`methySet` | `GenomicRatioSet` to be used to fill the slot.
`snpSet` | `SnpSet` to be used to fill the slot.
`x` | `MultiDataSet`
`unify.names` | Logical indicating if sample names of the sets should be unified.
`commonSamples` | Logical to indicate if common samples are selected
`i` | Character corresponding to selected sample names. They should match the id column of phenoData.
`j` | Character with the name of the selected tables.
`k` | `GenomicRange` used to filter the features.
`drop` | If TRUE, sets with no samples or features will be discarded
`feat` | Logical expression indicating features to keep
`phe` | Logical expression indicating the phenotype of the samples to keep
`keep` | If FALSE, sets where the expression cannot be evaluated will be discarded.

### Details

The names of the three lists (`assayData`, `phenoData` and `featureData`) must be the same.

### Value

`MultiDataSet`

`MultiDataSet`

### Methods (by generic)

- `add_eset`: Method to add an `eSet` to `MultiDataSet`.

- `add_genexp`: Method to add a slot of expression to `MultiDataSet`.

- `add_rnaseq`: Method to add a slot of (RNASeq) expression to `MultiDataSet`.

- `add_methy`: Method to add a slot of methylation to `MultiDataSet` from a `GenomicRatioSet`.

- `add_rse`: Method to add a `RangedSummarizedExperiment` to `MultiDataSet`.

- `add_se`: Method to add a `SummarizedExperiment` to `MultiDataSet`.

- `add_snps`: Method to add a slot of SNPs to `MultiDataSet`.

- `add_table`: Method to add a `matrix` to `MultiDataSet`.

- `as.list`: Returns a list with the first matrix of each dataset.

- `commonIds`: Get the name of the ids common to all datasets

- `commonSamples`: Get a MultiDataSet only with the samples present in all the tables

- `dims`: Returns the dimensions of the sets

- `w_iclusterplus`: Apply iClusterPlus clustering method to a MultiDataSet object

- `length`: Returns the number of sets into the object.

- `w_mcia`: Apply mcia integration method to a MultiDataSet object

- `names`: Get the names of the slots.

- `ncol`: Get number of samples of each set

- `nrow`: Get number of features of each set

- `rowRangesElements`: Get the name of the datasets that have rowRanges

- `sampleNames`: Get sample names

- `assayData`: Retrieve all assay data blocks.

- `fData`: Retrieve information on features.

- `featureData`: Retrieve information on features.

- `pData`: Retrieve information on experimental phenotypes

- `phenoData`: Retrieve information on experimental phenotypes

- `rowRanges`: Retrieve information on feature ranges.

- `[[`: Get a set from a slot

- `[`: Subset a MultiDataSet

- `subset`: Filter a subset using feature ids or phenotypes

### Slots

`assayData`

  List of `assayData` elements.

`phenoData`

  List of `AnnotatedDataFrame` containing the phenoData of each `assayData`.

`featureData`

  List of `AnnotatedDataFrame` containing the featureData of each `assayData`.

`rowRanges`

  List of `GenomicRanges` containing the rowRanges of each `assayData`.

`extraData`

  List of other slots of the original object.

`return_method`

  List of functions used to create the original object.

### See Also

`add_eset`, `add_rse`

### Examples

    createMultiDataSet()

[Package MultiDataSet version 1.14.0 Index]