register: Generic method to register data to the data server

In epivizrData: Data Management API for epiviz interactive visualization app

Description

Generic method to register data to the data server

Usage

register(object, columns = NULL, ...)

## S4 method for signature 'GenomicRanges'
register(object, columns, type = c("block", "bp", "gene_info"), ...)

## S4 method for signature 'RangedSummarizedExperiment'
register(object, columns = NULL, assay = 1, metadata = NULL)

## S4 method for signature 'ExpressionSet'
register(object, columns, annotation = NULL, assay = "exprs")

## S4 method for signature 'OrganismDb'
register(object, kind = c("gene", "tx"), keepSeqlevels = NULL, ...)

## S4 method for signature 'TxDb'
register(object, kind = c("gene", "tx"), keepSeqlevels = NULL, ...)

## S4 method for signature 'EnsDb'
register(object, kind = c("gene", "tx"), keepSeqlevels = NULL, ...)

## S4 method for signature 'data.frame'
register(object, columns = NULL, ...)

Arguments

object	The object to register to data server
columns	Name of columns containing data to register
...	Additonal arguments passed to object constructors
type	Which type of data object to register for a GenomicRanges object. block: only region data, bp base-pair resolution quantitative data (see columns argument), geneInfo information about gene location.
assay	Which assay in object to register
metadata	Additional metadata about features
annotation	Character string indicating platform annotation (only hgu133plus2 supported for now)
kind	Make gene or transcript annotation (only gene supported for now)
keepSeqlevels	character vector indicating seqlevels in object to keep

Value

Object inheriting from EpivizData class

Methods (by class)

• GenomicRanges: Register a GenomicRanges object

• RangedSummarizedExperiment: Register a RangedSummarizedExperiment object

• ExpressionSet: Register an ExpressionSet object

• OrganismDb: Register an OrganismDb object

• TxDb: Register a TxDb object

• EnsDb: Register an EnsDb object

• data.frame: Register an data.frame

Examples

library(GenomicRanges)
# create an example GRanges object
gr <- GRanges("chr10", IRanges(start=1:1000, width=100), score=rnorm(1000))
# this returns an EpivizData object without adding to data manager
# this is not the preferred way of creating these object, but is shown
# here for completeness.
ms_obj <- epivizrData:::register(gr, type="bp", columns="score") 

server <- epivizrServer::createServer(port=7123L)
data_mgr <- epivizrData::createMgr(server)

# This adds a data object to the data manager
data_mgr$add_measurements(gr, "example_gr", type="bp", columns="score")

epivizrData documentation built on Nov. 8, 2020, 7:36 p.m.