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

1. load peaks file: GenomeFeatures::readPeakFile.

2. Build a convenient object for find overlaps beetween all selected features and genomic coordinates targets: GenomeFeatures::build_genome_features.

3. Find overlaps beetween genomic coordinates and features: GenomeFeatures::genome_features_overlaps.

4. Features plot: GenomeFeatures::Plot.

5. Get annotation table: GenomeFeatures::Table.

6. Features ovelaps.