listPredefinedDataSets: List predefined datasets

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

List predefined datasets

Description

Use listPredefinedDataSets() to receive a vector of names for predefined datasets that can be aquired from AnnotationHub that are already correctly parsed and formatted. Each of the listed names can be used as input for addDataSetFromHub(). Currently supported:

• protCodingGenes - Protein coding genes from HG19 (GRCh37) Ensembl For additional information use: getInfoOnIds(AnnotationHub(), "AH10684")

• CGI - CpG islands from HG19 UCSC For additional information use: getInfoOnIds(AnnotationHub(), "AH5086")

• SNP - Common Single Nucleotide Polymorphism from HG19 UCSC For additional information use: getInfoOnIds(AnnotationHub(), "AH5105")

• TFBS - Transcription Factor Binding Sites conserved from HG19 UCSC For additional information use: getInfoOnIds(AnnotationHub(), "AH5090")

• Promoters - Promoter and flanking regions from HG19 Ensembl (Note: This annotation is currently not included in AnnotationHub and is therefore downloaded from Ensembl's ftp site)

Usage

listPredefinedDataSets()

Value

character vector.

Examples

listPredefinedDataSets()

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