epivizr (version 2.2.3)

register: Generic method to register data to the data server

Description

Generic method to register data to the data server

Usage

register(object, columns = NULL, ...)
## S3 method for class 'GenomicRanges':
register(object, columns, type = c("block", "bp",
  "gene_info"), ...)
## S3 method for class 'RangedSummarizedExperiment':
register(object, columns = NULL,
  assay = 1, metadata = NULL)
## S3 method for class 'ExpressionSet':
register(object, columns, annotation = NULL,
  assay = "exprs")
## S3 method for class 'OrganismDb':
register(object, kind = c("gene", "tx"),
  keepSeqlevels = NULL, ...)
## S3 method for class 'TxDb':
register(object, kind = c("gene", "tx"),
  keepSeqlevels = 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 aGenomicRangesobject
• RangedSummarizedExperiment: Register aRangedSummarizedExperimentobject
• ExpressionSet: Register anExpressionSetobject
• OrganismDb: Register anOrganismDbobject
• TxDb: Register aTxDbobject

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")