example_GRanges

datasets

data

Based on external numerous data files where rfPred scores
are pre-calculated on all genomic positions of the human exome,
the package gives rfPred scores to missense variants identified
by the chromosome, the position (hg19 version), the referent
and alternative nucleotids and the uniprot identifier of the
protein. Note that for using the package, the user has to be
connected on the Internet or to download the TabixFile and
index (approximately 3.3 Go).

Hugo Varet

rfPred

Assign rfPred functional prediction scores to a missense
variants list

example_GRanges function

A <code>GRanges</code> object with 11 rows and several columns:
  <dl>
    <dt><code>seqnames</code></dt><dd>Chromosome number (only <code>Y</code> in this example)</dd> <dt><code>ranges</code></dt><dd><code>IRanges</code> object for which <code>start</code>=<code>end</code>: position on the chromosome</dd> <dt><code>reference</code></dt><dd>Referent nucleotid (<code>A</code>, <code>C</code>, <code>G</code> or <code>T</code>)</dd> <dt><code>alteration</code></dt><dd>Alteration nucleotid (<code>A</code>, <code>C</code>, <code>G</code> or <code>T</code>)</dd> </dl>

example_GRanges: Toy example of GRanges object

Description

Arguments

Format