


GenomeFeatures R package
The aim of this package is to provide a full genomic features annotation from genomic coordinates, without use an annotation priority.
Installation
## using install_gitlab
remotes::install_gitlab(
"aurelien.brionne/GenomeFeatures",
host = "forgemia.inra.fr",
build_opts = c("--no-resave-data", "--no-manual")
)
## alternative (from local directory)
# clone package (from prompt)
git clone https://forgemia.inra.fr/aurelien.brionne/GenomeFeatures.git
# build package (from R console)
devtools::build("GenomeFeatures")
# install package (from R console)
install.packages("GenomeFeatures_1.1.tar.gz", repos = NULL, type = "source")
Quick overview
-
load peaks file:
GenomeFeatures::readPeakFile
. -
Build a convenient object for find overlaps beetween all selected features and genomic coordinates targets:
GenomeFeatures::build_genome_features
. -
Find overlaps beetween genomic coordinates and features:
GenomeFeatures::genome_features_overlaps
. -
Features plot:
GenomeFeatures::Plot
.
- Get annotation table:
GenomeFeatures::Table
.
- Features ovelaps.