README.md

In rqtl/qtl2bioc: Connect to Bioconductor for QTL Experiments

R/qtl2bioc

Karl Broman

qtl2bioc is part of R/qtl2. It uses Bioconductor facilities to obtain the set of mouse genes in a region. While the functions within qtl2bioc could logically be included within qtl2, we've kept it separate in order to reduce package dependencies for those not interested in making use of the Bioconductor features.

Installation

To install qtl2bioc, first install the Bioconductor packages GenomicRanges and AnnotationHub:

install.packages("BiocManager")
BiocManager::install(c("GenomicRanges", "AnnotationHub"))

Next, install the remotes package:

install.packages("remotes")

Finally, install the R/qtl2bioc package from its Github repository.

remotes::install_github("rqtl/qtl2bioc")

Usage

The R/qtl2bioc package contains two key functions, grab_ensembl(), for downloading the Ensembl gene annotations, and create_ensembl_query_func(), for creating a query function to grab gene records for a given region.

License

Licensed under GPL-3.

rqtl/qtl2bioc documentation built on Jan. 2, 2021, 1:53 a.m.