loadAnnotations: Load annotation datasets

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

Load annotation datasets

Description

Load dataset files containing genomic regions annotation information from hard drive. loadAnnotations calls readQuery and readSubject to read in genomic regions as GenomicRanges objects stored as .RDS / .rds files. Each region needs chromosome, start, end and strand information. A unique ID and a name column must be present in the GenomicRanges object metadata. OGRE searches for the query file in your query folder and any number of subject files in your subjects folder. Alternatively, .gff (v2&v3) files in the query or subject folder with attribute columns containing "ID" and "name" information are read in by OGRE.

Usage

loadAnnotations(OGREDataSet)

Arguments

OGREDataSet

A OGREDataSet.

Value

A OGREDataSet.

Examples

myOGRE <- makeExampleOGREDataSet()
myOGRE <- loadAnnotations(myOGRE)

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