register-methods: Encapsulate data object in Epiviz
In epiviz/epivizr-release: R Interface to epiviz web app

Description Usage Arguments Details Value Author(s) See Also

This method encapsulates data objects in R/bioc to be used for interactive visualization. It converts GenomicRanges objects to GIntervalTree objects when appropriate. It returns objects from the EpivizData-class hierarchy.

## S4 method for signature 'GenomicRanges'
register(object, columns=NULL, type=c("block", "bp", "geneInfo"), ...)
## S4 method for signature 'SummarizedExperiment'
register(object, columns=NULL, assay=1)
## S4 method for signature 'ExpressionSet'
register(object, columns=NULL, annotation=NULL)
## S4 method for signature 'OrganismDb'
register(object, kind=c("gene", "tx"), keepSeqlevels=NULL, ...)

`object`	data object to encapsulate
`columns`	columns in object to use. All columns are used if `NULL`
`type`	for `GenomicRanges` objects, use block representation, base-pair level quantitative representation, or gene annotation (see below)
`assay`	for `SummarizedExperiment` and `ExpressionSet` objects, determine which `assay` to use
`annotation`	for `ExpressionSet` objects, determine the annotation to use to obtain feature genomic coordinates. If `NULL`, then `annotation(object)` is used
`kind`	for `OrganismDb` objects, return a "gene" or "transcript" annotation. Only gene annotations are currently supported.
`keepSeqlevels`	for `OrganismDb` objects, a list of seqnames to retain in the gene annotation. See `keepSeqlevels`

...

arguments passed to EpivizData-class subclasses constructors

This function converts GenomicRanges objects to GIntervalTree objects when appropriate. For example, the rowData slot in SummarizedExperiment objects. Genomic coordinates for features in ExpressionSet objects are obtained used the AnnotationDb interface from the provided annotation.

Gene Annotations: Gene annotations can be provided throughGenomicRanges (using type="geneInfo") or OrganismDb objects. For the latter, we assume a Gene (character) column is available containing gene names, and a Exons (IRangesList) column is available. Annotations using GRangesList objects will be supported in the near future.

Returns objects from the EpivizData-class hierarchy depending on the provided object. When object is a GenomicRanges object and type=="block", a EpivizBlockData-class object is returned; a EpivizBpData-class object is returned if type=="bp". For SummarizedExperiment and ExpressionSet objects, a EpivizFeatureData-class object is returned. For SummarizedExperiment objects, columns SYMBOL and PROBEID are assumed to be present in mcols(rowData(object)).