hiAnnotator

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see hiAnnotator.

Functions for annotating GRanges objects.

Bioconductor version: 3.0

hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.

Author: Nirav V Malani <malnirav at gmail.com>

Maintainer: Nirav V Malani <malnirav at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hiAnnotator")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("hiAnnotator")

Details

Package Archives

Follow Installation instructions to use this package in your R session.