availableGScores: Exploring genomic scores resources

In rcastelo/GenomicScores: Infrastructure to work with genomewide position-specific scores

Exploring genomic scores resources

Description

Functions to explore genomic scores resources.

Usage

availableGScores(use.internet=FALSE)
getGScores(x, accept.license=FALSE)

Arguments

x	Acharacter vector of length 1 specifiying the genomic scores resource to fetch.
use.internet	A logical value specifying whether we want to check through the internet whether the annotation packages and AnnotationHub resources are ready to be downloaded. By default, i.e. use.internet=FALSE, this is not checked to speed up the execution of this function.
accept.license	A logical value specifying whether we accept the license under which we can use the requested data, when the data is distributed under such a license.

Details

The function availableGScores() shows genomic score sets available as AnnotationHub online resources.

Value

The function availableGScores() returns a data.frame object with a row for each available resource of genomic scores and the following four columns:

• Name: Name of the Bioconductor package or AnnotationHub resource.

• Organism: Organism on which the genomic scores are defined.

• Category: Category to which the genomic scores belong to.

• Installed: Whether the resource is installed as a package (TRUE) or not (FALSE).

• Cached: Whether the resource is available within the local cache of the AnnotationHub (TRUE) or not (FALSE).

• BiocManagerInstall: Whether the resource can be installed as an annotation package through BiocManager::install() (TRUE) or not (FALSE).

• AnnotationHub: Whether the resource can be downloaded as a GScores object through the AnnotationHub, using the function getGScores() (TRUE), or not (FALSE).

The function getGScores() returns a GScores object.

Author(s)

R. Castelo

References

Puigdevall, P. and Castelo, R. GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor. Bioinformatics, 18:3208-3210, 2018.

See Also

getGScores() phastCons100way.UCSC.hg38 MafDb.1Kgenomes.phase1.hs37d5

Examples

availableGScores()

## Not run: 
gsco <- getGScores("cadd.v1.6.hg38")

## End(Not run)

rcastelo/GenomicScores documentation built on May 5, 2024, 11:38 a.m.