register {epivizrData} | R Documentation |
Generic method to register data to the data server
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, ...)
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 |
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 |
Object inheriting from EpivizData
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
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")