variant_list_Y

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

variant_list_Y function

A data frame with 5 observations on the following 5 variables:
  <dl>
    <dt><code>chr</code></dt><dd>Chromosome number (only <code>Y</code> in this example)</dd> <dt><code>pos</code></dt><dd>Position on the chromosome (numeric)</dd> <dt><code>ref</code></dt><dd>Referent nucleotid (<code>A</code>, <code>C</code>, <code>G</code> or <code>T</code>)</dd> <dt><code>alt</code></dt><dd>Alteration nucleotid (<code>A</code>, <code>C</code>, <code>G</code> or <code>T</code>)</dd> <dt><code>uniprot</code></dt><dd>Uniprot protein identifier (factor)</dd> </dl>

variant_list_Y: Toy example of data.frame

Description

Arguments

Format