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<h3>vcfR documentation</h3>
by
<br>
Brian J. Knaus and Niklaus J. Grünwald
</center>
</p>
<div id="header">
<h1 class="title toc-ignore">Extract data</h1>
</div>
<div id="TOC">
<ul>
<li><a href="#extracting-data-matrices"
id="toc-extracting-data-matrices">Extracting data matrices</a></li>
<li><a href="#querying-the-meta-data"
id="toc-querying-the-meta-data">Querying the meta data</a></li>
<li><a href="#extract-depth-dp" id="toc-extract-depth-dp">Extract depth
(DP)</a></li>
</ul>
</div>
<div id="extracting-data-matrices" class="section level2">
<h2>Extracting data matrices</h2>
<p>The vcfR function <code>extract.gt()</code> is used to extract
matrices of data from the GT portion of VCF data. The funtion
<code>extract.gt()</code> provides a link between VCF data and R. Much
of R is designed to operate on matrices of data and once
<code>extract.gt()</code> provides this matrix the universe of R becomes
available.</p>
</div>
<div id="querying-the-meta-data" class="section level2">
<h2>Querying the meta data</h2>
<p>As an example of how to use <code>extract.gt()</code> we will extract
the depth (DP) data. Note that we use the ‘as.numeric=TRUE’ option here.
We should only use this option when we are certain that we have numeric
data. If you use it on non-numeric data R will do its best to do
something, which is not likely to be what you expect. We can use the
<code>queryMETA()</code> function remind us what this element is.</p>
<pre class="r"><code>queryMETA(vcf, element = 'FORMAT.+DP')</code></pre>
<pre><code>## [[1]]
## [1] "FORMAT=ID=DP"
## [2] "Number=1"
## [3] "Type=Integer"
## [4] "Description=Read Depth (only filtered reads used for calling)"</code></pre>
<p>The <code>queryMETA()</code> function reports a description to tell
us what the acronym ‘DP’ means. It also reports the type of data this
is. Here we see that ‘DP’ is integer data. Because integers are a form
of numerics we can safely use <code>as.numeric = TRUE</code>.</p>
</div>
<div id="extract-depth-dp" class="section level2">
<h2>Extract depth (DP)</h2>
<p>The GT portion of VCF data is not strictly tabular. We can observe
this by accessing the <code>@gt</code> slot of the vcfR object.</p>
<pre class="r"><code>vcf@gt[1:4,1:4]</code></pre>
<pre><code>## FORMAT 1 10
## [1,] "GT:AD:DP:GQ:PL" "0/0:5,0:5:96:0,15,180" "1/1:0,10:10:99:255,30,0"
## [2,] "GT:AD:DP:GQ:PL" "1/1:0,1:1:66:36,3,0" "0/0:4,0:4:94:0,12,144"
## [3,] "GT:AD:DP:GQ:PL" NA NA
## [4,] "GT:AD:DP:GQ:PL" "1/1:0,5:5:96:180,15,0" "0/0:8,0:8:99:0,24,255"
## 13
## [1,] "0/0:9,0:9:99:0,27,255"
## [2,] "0/0:1,0:1:66:0,3,36"
## [3,] "0/0:3,0:3:88:0,9,108"
## [4,] NA</code></pre>
<p>The first column reports the format for subsequent columns. This is a
colon delimited string containing abbreviations for the data that appear
in subsequent columns, in the same order as they appear in subsequent
columns. Different variants (rows) can have different formats, so these
need to be processed independently. The <code>extract.gt()</code>
function finds which position the data you’re interested in is in the
format string and processes this position in the subsequent columns.
Here we’ve also used the option to convert the data to numerical data.
The default is to leave the data as character data.</p>
<pre class="r"><code>dp <- extract.gt(vcf, element = "DP", as.numeric=TRUE)
dp[1:4,1:3]</code></pre>
<pre><code>## 1 10 13
## S1_4509 5 10 9
## S1_4657 1 4 1
## S1_5193 NA NA 3
## S1_5647 5 8 NA</code></pre>
<p>We now have a matrix of numerical ‘DP’ data with the sample names as
column names. Samples (columns) or variants (rows) can be accessed with
the square brackets (<code>[,]</code>). If you need a matrix where the
samples are in rows and the variants are in columns you can use the
transpose function (<code>t()</code>). We have now taken our VCF data
and extracted it into a form that makes it available to much of the
broad spectrum of existing R packages and functions.</p>
</div>
<center>
<hr class="style1">
<p>Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.</p>
<p>USDA Agricultural Research Service, Horticultural Crops Research Lab.</p>
</center>
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