epivizr (version 1.4.6)

register-methods: Encapsulate data object in Epiviz

Description

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.

Usage

"register"(object, columns=NULL, type=c("block", "bp", "geneInfo"), ...)
"register"(object, columns=NULL, assay=1)
"register"(object, columns=NULL, annotation=NULL)
"register"(object, kind=c("gene", "tx"), keepSeqlevels=NULL, ...)

Arguments

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

Value

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)).

Details

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.

See Also

EpivizData-class and subclasses, EpivizDeviceMgr-class, GenomicRanges, SummarizedExperiment, GIntervalTree, OrganismDb ExpressionSet