# Opportunity matrix

Opportunity matrix is a tab-delimited text file with a matrix of counts of trinucleotide contexts found in studied genomes. It must structured as the SNV matrix, with mutations specified on the head line (for each SNV count, the Opportunity matrix shows the total number of genomic loci where the refered mutation could have occurred) . The Opportunity matrix can be generated from a VCF file, see signeR documentation. The table below shows a example of the opportunity matrix structure.

<table class="table table-striped table-hover" style="margin-left: auto; margin-right: auto;">
 <thead>
  <tr>
   <th style="text-align:left;"> 366199887 </th>
   <th style="text-align:left;"> 211452373 </th>
   <th style="text-align:left;"> 45626142 </th>
   <th style="text-align:left;"> 292410567 </th>
   <th style="text-align:left;"> 335391892 </th>
   <th style="text-align:left;"> 239339768 </th>
   <th style="text-align:left;"> ... </th>
   <th style="text-align:left;"> 50233875 </th>
  </tr>
 </thead>
<tbody>
  <tr>
   <td style="text-align:left;"> 202227618 </td>
   <td style="text-align:left;"> 116207171 </td>
   <td style="text-align:left;"> 25138239 </td>
   <td style="text-align:left;"> 161279580 </td>
   <td style="text-align:left;"> 184193767 </td>
   <td style="text-align:left;"> 131051208 </td>
   <td style="text-align:left;"> ... </td>
   <td style="text-align:left;"> 177385805 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 225505378 </td>
   <td style="text-align:left;"> 130255706 </td>
   <td style="text-align:left;"> 28152934 </td>
   <td style="text-align:left;"> 179996700 </td>
   <td style="text-align:left;"> 206678032 </td>
   <td style="text-align:left;"> 147634427 </td>
   <td style="text-align:left;"> ... </td>
   <td style="text-align:left;"> 199062504 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 425545790 </td>
   <td style="text-align:left;"> 245523433 </td>
   <td style="text-align:left;"> 53437284 </td>
   <td style="text-align:left;"> 339065644 </td>
   <td style="text-align:left;"> 389386002 </td>
   <td style="text-align:left;"> 278770926 </td>
   <td style="text-align:left;"> ... </td>
   <td style="text-align:left;"> 375075216 </td>
  </tr>
  <tr>
   <td style="text-align:left;"> 452332390 </td>
   <td style="text-align:left;"> 259934779 </td>
   <td style="text-align:left;"> 55862550 </td>
   <td style="text-align:left;"> 361010972 </td>
   <td style="text-align:left;"> 412168035 </td>
   <td style="text-align:left;"> 292805460 </td>
   <td style="text-align:left;"> ... </td>
   <td style="text-align:left;"> 396657807 </td>
  </tr>
</tbody>
</table>

You can create a opportunity matrix from the reference genome using the method 
```R
genOpportunityFromGenome
```
from signeR package. See the [documentation](https://bioconductor.org/packages/release/bioc/vignettes/signeR/inst/doc/signeR-vignette.html#toc3) for more details. 

## Columns
There is no header in this file and each column represents a trinucleotide context.

## Rows
Each row contains the count frequency of the trinucleotides in the whole analyzed region for each sample.

## Example file

[21 breast cancer](https://raw.githubusercontent.com/rvalieris/signeR/master/inst/extdata/21_breast_cancers.opportunity.txt)