registerFeatureSetCollections {iSEEu} | R Documentation

## Register feature set collections

### Description

Register feature set collations and their annotations for display in FeatureSetTables.

### Usage

    registerFeatureSetCollections(se, collections)

    registerFeatureSetCommands(se, commands)

    getFeatureSetCollections(se)

    getFeatureSetCommands(se)

### Arguments

`se` | The SummarizedExperiment object to be used in `iSEE`.
`collections` | A named list containing one or more CharacterList objects. Each entry represents a collection of feature sets (see Details) and should be named.
`commands` | A named list containing two character vectors of commands to use to generate collections and sets.

### Details

Arbitrary feature sets are challenging as there is no obvious place to store them. `registerFeatureSetCollections` and friends will insert these sets into the `metadata` of the SummarizedExperiment object, allowing the corresponding getter functions to quickly extract them later within the `iSEE` app.

`collections` should be a named list containing CharacterList objects. Each CharacterList represents a collection where each entry is a feature set, i.e., a character vector corresponding to some of the row names of `se`. The `mcols` can contain additional per-set fields (e.g., descriptions, enrichment statistics) that will be shown in the FeatureSetTable.

`commands` should be a list containing:

- `collections`, a named character vector where each entry is named after a feature set collection. Each entry should be a string containing R commands to define a data.frame named `tab`, where each row is a feature set and the row names are the names of those sets.

- `sets`, a character vector where each entry is named after a feature set collection in the same order as `commands$collections`. Each entry should be a string containing R commands to define a character vector named `selected` containing the identity of all rows of the SummarizedExperiment in the set of interest. (These commands can assume that a `.set_id` variable is present containing the name of the chosen feature set, as well as the `se` variable containing the input SummarizedExperiment object.)

If neither `collections` nor `commands` are provided, any previously registered content in `se` is removed.

### Value

For `registerFeatureSetCollections` and `registerFeatureSetCommands`, a modified `se` is returned that contains the feature set collections or commands, respectively. This can be used with FeatureSetTables in `iSEE` calls.

For `getFeatureSetCollections`, the list of CharacterLists is returned. Alternatively `NULL`, if no such list was stored by `registerFeatureSetCollections`.

For `getFeatureSetCommands`, the list of of commands is returned containing `collections` and `sets`. Alternatively `NULL`, if no such list was stored by `registerFeatureSetCommands`.

### Author(s)

Aaron Lun

### Examples

    library(scRNAseq)
    sce <- LunSpikeInData(location=FALSE)

    # Make up some random collections.
    random <- CharacterList(
       Aaron = sample(rownames(sce), 10),
       Kevin = sample(rownames(sce), 20),
       Charlotte = sample(rownames(sce), 30),
       Fed = sample(rownames(sce), 40)
    )
    mcols(random)$p.value <- runif(4)

    # Storing the collections inside our SummarizedExperiment.
    sce <- registerFeatureSetCollections(sce, list(random=random))
    getFeatureSetCollections(sce)

    if (interactive()) {
        iSEE(sce, initial=list(FeatureSetTable()))
    }

[Package iSEEu version 1.4.0 Index]