get.ensembl.annotation {GRIN2} | R Documentation |
Get Ensembl Gene and Regulatory Features Annotation Data
Description
Retrieves gene and regulatory feature annotation data from the Ensembl BioMart database for the Human GRCh38 (hg38) genome assembly using the biomaRt package.
Usage
get.ensembl.annotation(genome.assembly)
Arguments
genome.assembly |
Character string. Currently, only |
Details
This function retrieves:
Gene annotation: Ensembl ID, chromosome, start/end positions, gene name, description, biotype, strand, and cytogenetic band.
Predicted regulatory features: Promoters, enhancers, CTCF binding sites, etc., from the Ensembl regulatory build.
Validated regulatory features: Experimentally confirmed enhancers and TSSs from the FANTOM5 project.
Value
A list with three components:
- gene.annotation
Data frame of gene-level annotation.
- reg.annotation.predicted
Data frame of predicted regulatory features.
- reg.annotation.validated
Data frame of validated regulatory features (FANTOM5).
Author(s)
Abdelrahman Elsayed abdelrahman.elsayed@stjude.org and Stanley Pounds stanley.pounds@stjude.org
References
Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.
Zerbino, Daniel R., et al. (2015). The ensembl regulatory build.
Kinsella, Rhoda J., et al. (2011). Ensembl BioMarts: a hub for data retrieval across taxonomic space.
See Also
Examples
hg38.ann <- get.ensembl.annotation("Human_GRCh38")
# gene level annotations:
hg38.genes <- hg38.ann$gene.annotation
# regulatory sequences from the ensembl genome build:
hg38.reg.pred <- hg38.ann$reg.annotation.predicted
# regulatory sequences from the FANTOM5 project:
hg38.reg.val <- hg38.ann$reg.annotation.validated