sites

A sample dataset containing collection of unique HIV & MLV integration sites
in the human genome mapped to UCSC freeze hg18 from PMID: 12805549.

datasets

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.

Nirav V Malani

hiAnnotator

Functions for annotating GRanges objects

sites function

A data frame with 1303 rows and 5 variables

format

<url>http://www.ncbi.nlm.nih.gov/pubmed/?term=12805549</url>

sites: Sample Retrovirus Integration Sites data

Description

Arguments

format

source

Details