CellBaseParam-class: CellBaseParam Class

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

CellBaseParam Class

Description

This class defines a CellBaseParam object to hold filtering parameters.

Details

This class stores parameters used for filtering the CellBaseR query and is avaialable for all query methods. CellBaseParam object is used to control what results are returned from the' CellBaseR methods

Slots

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

See Also

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

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