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:

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]