local_metadata: Locate local metadata outside of AnnotationHub

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

Locate local metadata outside of AnnotationHub

Description

Locate local metadata outside of AnnotationHub

Usage

local_metadata(local_path = "/dcl01/lieber/ajaffe/lab/GenomicState/data-raw")

Arguments

local_path

A character(1) pointing to where the data is stored locally

Value

The AnnotationHub metadata data.frame() for the data in this package with RDataPath updated to point to the local_path. It includes an addtional column called loadCode which you can evaluate with eval(parse(text = entry)).

Author(s)

Leonardo Collado-Torres

See Also

AnnotationHubData::makeAnnotationHubMetadata()

Examples

## Get the local metadata
meta <- local_metadata()

## Subset to the data of interest, lets say hg19 TxDb for v31
interest <- subset(meta, RDataClass == "TxDb" & Tags == "Gencode:v31:hg19")

## Inspect the result
interest

## Next you can load the data
if (file.exists(interest$RDataPath)) {
    ## This only works at JHPCE
    eval(parse(text = interest$loadCode))

    ## Explore the loaded object (would be gencode_v31_hg19_txdb in this case)
    gencode_v31_hg19_txdb
}

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