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 "Human_GRCh38" is supported.

Details

This function retrieves:

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

useEnsembl, getBM

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


[Package GRIN2 version 2.0.0 Index]