getUCSCtable

Name of the annotation table as it appears on UCSC browser.

tableName

Name of the track annotation table as it appears in on
UCSC browser.

trackName

UCSC session object returned by <code><a href="/link/makeUCSCsession?package=hiAnnotator&version=1.6.2" rd-options="" data-mini-rdoc="hiAnnotator::makeUCSCsession">makeUCSCsession</a></code>
or <code><a href="/link/browserSession?package=hiAnnotator&version=1.6.2" rd-options="" data-mini-rdoc="hiAnnotator::browserSession">browserSession</a></code>. If left NULL the function will call
<code><a href="/link/makeUCSCsession?package=hiAnnotator&version=1.6.2" rd-options="" data-mini-rdoc="hiAnnotator::makeUCSCsession">makeUCSCsession</a></code> with the provided freeze to initiate a session.

bsession

one of following: hg18, mm8, rheM, etc. Default is hg18.

freeze

Arguments to be passed to <code><a href="/link/ucscTableQuery?package=hiAnnotator&version=1.6.2" rd-options="" data-mini-rdoc="hiAnnotator::ucscTableQuery">ucscTableQuery</a></code>.

Obtain a UCSC annotation table given the table & track name.

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

getUCSCtable function

UCSC session object returned by <code><a href="makeUCSCsession" rd-options="">makeUCSCsession</a></code>
or <code><a href="browserSession" rd-options="">browserSession</a></code>. If left NULL the function will call
<code><a href="makeUCSCsession" rd-options="">makeUCSCsession</a></code> with the provided freeze to initiate a session.

Arguments to be passed to <code><a href="ucscTableQuery" rd-options="">ucscTableQuery</a></code>.

getUCSCtable: Obtain a UCSC annotation table given the table & track name.

Description

Usage

Arguments

Value

See Also

Examples