CellBaseParam: A Constructor for the CellBaseParam Object

Description Usage Arguments Value See Also Examples

View source: R/CellBaseParam-methods.R

Description

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

Usage

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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

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

cellbaseR documentation built on Nov. 8, 2020, 5:38 p.m.