gtars-r

R bindings for gtars functionality, providing an R API for genomic interval analysis.

Installation

To install the development version, use the remotes package:

install.packages("remotes")
remotes::install_github("databio/gtars", ref = "dev", subdir = "gtars-r")

You can also install the R package locally from the repo directory:

R CMD INSTALL gtars-r

Available Modules

refget

library(gtars)

# Compute sequence digest
readable <- 'ACGTACGT'
gtars::sha512t24u_digest(readable)
gtars::md5_digest(readable)

# Use RefgetStore for sequence management
store <- global_refget_store('raw')

IGD

library(gtars)

### Building an Index
igd_create(output_path = '/home/igd_output/', filelist = '/home/my_bedfiles/')

### Querying with a single bed file
igd_search(database_path = 'my_igd_database.igd', query_path = 'my_query.bed')