GenomicStateHub: Access GenomicState objects through AnnotationHub

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

Access GenomicState objects through AnnotationHub

Description

This function uses AnnotationHub to obtain the objects provided by this package. These are: the TxDb object made with gencode_txdb(), the annotated genes object made with gencode_annotated_genes() or the GenomicState object made with gencode_genomic_state().

Usage

GenomicStateHub(
  version = "31",
  genome = c("hg38", "hg19"),
  filetype = c("TxDb", "AnnotatedGenes", "GenomicState"),
  ah = AnnotationHub::AnnotationHub()
)

Arguments

version	A character(1) with the Gencode version number.
genome	A character(1) with the human genome version number. Valid options are 'hg38' or 'hg19'.
filetype	A character() with either TxDb, AnnotatedGenes or GenomicState.
ah	An AnnotationHub object AnnotationHub-class.

Value

The AnnotationHub-class query for the file you requested.

Author(s)

Leonardo Collado-Torres

See Also

gencode_txdb() gencode_annotated_genes() gencode_genomic_state()

Examples

## Query AnnotationHub for the GenomicState object for Gencode v31 on
## hg19 coordinates
hub_query_gs_gencode_v31_hg19 <- GenomicStateHub(
    version = "31",
    genome = "hg19",
    filetype = "GenomicState"
)
hub_query_gs_gencode_v31_hg19


## Check the metadata
mcols(hub_query_gs_gencode_v31_hg19)

## Access the file through AnnotationHub
if (length(hub_query_gs_gencode_v31_hg19) == 1) {
    hub_gs_gencode_v31_hg19 <- hub_query_gs_gencode_v31_hg19[[1]]

    hub_gs_gencode_v31_hg19
}

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