gencode_annotated_genes: Annotation the genes for a given Gencode TxDb object

In LieberInstitute/GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode

Annotation the genes for a given Gencode TxDb object

Description

Based on a TxDb object built by gencode_txdb() this function annotates the genes. This information is then used by packages like derfinder and derfinderPlot.

Usage

gencode_annotated_genes(txdb)

Arguments

txdb	A GenomicFeatures::TxDb object built with gencode_txdb().

Value

The annotated genes resulting from bumphunter::annotateTranscripts().

Author(s)

Leonardo Collado-Torres.

References

Based on code for the brainflowprobes package at: https://github.com/LieberInstitute/brainflowprobes/blob/devel/data-raw/create_sysdata.R

See Also

gencode_txdb() gencode_genomic_state()

Examples

## Start from scratch if you want:
## Not run: 
txdb_v31_hg19_chr21 <- gencode_txdb("31", "hg19", chrs = "chr21")

## End(Not run)

## or read in the txdb object for hg19 chr21 from this package
txdb_v31_hg19_chr21 <- AnnotationDbi::loadDb(
    system.file("extdata", "txdb_v31_hg19_chr21.sqlite",
        package = "GenomicState"
    )
)

## Obtain the annotated genes for the Gencode TxDb object
genes_v31_hg19_chr21 <- gencode_annotated_genes(txdb_v31_hg19_chr21)

## Explore the result
genes_v31_hg19_chr21

LieberInstitute/GenomicState documentation built on May 12, 2023, 5:15 p.m.