CellBaseParam: A Constructor for the CellBaseParam Object

In melsiddieg/cellbaseR: Querying annotation data from the high performance Cellbase web

A Constructor for the CellBaseParam Object

Description

CellBaseParam object is used to control what results are returned from the CellBaseR methods

Usage

CellBaseParam(
  assembly = character(),
  feature = character(),
  region = character(),
  rsid = character(),
  accession = character(),
  type = character(),
  mode_inheritance_labels = character(),
  clinsig_labels = character(),
  alleleOrigin = character(),
  consistency_labels = character(),
  so = character(),
  source = character(),
  trait = character(),
  include = character(),
  exclude = character(),
  limit = character()
)

Arguments

assembly	A character the assembly build to query, e.g.GRCh37(default)
feature	A character vector denoting the feature/s to be queried
region	A character vector denoting the region/s to be queried must be in the form 1:100000-1500000
rsid	A character vector denoting the rs ids to be queried
accession	A caharcter vector of Cinvar accessions
type	A caharcter vector of Variant types
mode_inheritance_labels	A character vector
clinsig_labels	A character vector
alleleOrigin	A character vector
consistency_labels	A character vector
so	A character vector denoting sequence ontology to be queried
source	A character vector
trait	A character vector denoting the trait to be queried
include	A character vector denoting the fields to be returned
exclude	A character vector denoting the fields to be excluded
limit	A number limiting the number of results to be returned

Value

an object of class CellBaseParam

See Also

https://github.com/opencb/cellbase/wiki and the RESTful API documentation http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/

Examples

cbParam <- CellBaseParam(assembly="GRCh38",feature=c("TP73","TET1"))
print(cbParam)

melsiddieg/cellbaseR documentation built on Jan. 16, 2024, 4:12 a.m.