availableGScores: Exploring genomic scores resources

View source: R/availableGScores.R

availableGScoresR Documentation

Exploring genomic scores resources


Functions to explore genomic scores resources.


getGScores(x, accept.license=FALSE)



Acharacter vector of length 1 specifiying the genomic scores resource to fetch.


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.


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.


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


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.


R. Castelo


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



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gsco <- getGScores("cadd.v1.6.hg38")

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