addDataSetFromHub: Add dataSet from AnnotationHub

In svenbioinf/OGRE: Calculate, visualize and analyse overlap between genomic regions

Add dataSet from AnnotationHub

Description

AnnotationHub offers a wide range of annotated datasets which can be manually aquired but need some parsing to work with OGRE as detailed in vignette section "Load datasets from AnnotationHub". For convienence addDataSetFromHub() adds one of the predefined human dataSets of listPredefinedDataSets() to a OGREDataSet.Those are taken from AnnotationHub and are ready to use for OGRE. Additional information on dataSets can be found here listPredefinedDataSets.

Usage

addDataSetFromHub(OGREDataSet, dataSet, type)

Arguments

OGREDataSet	OGREDataSet
dataSet	character Name of one predefined dataSets to add as query or subject to a OGREDataSet. Possible dataSets can be show with listPredefinedDataSets().
type	Type of dataSet, must be either query or subject. If query the dataSet will be added as query and at the first position of OGREDataSet.

Value

OGREDataSet.

Examples

myOGRE <- OGREDataSet() 
myOGRE <- addDataSetFromHub(myOGRE,"protCodingGenes","query")

svenbioinf/OGRE documentation built on Jan. 30, 2023, 10:55 p.m.