inst/extdata/opp_help.md

In rvalieris/signeR: Empirical Bayesian approach to mutational signature discovery

Opportunity matrix

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

366199887 211452373 45626142 292410567 335391892 239339768 ... 50233875 202227618 116207171 25138239 161279580 184193767 131051208 ... 177385805 225505378 130255706 28152934 179996700 206678032 147634427 ... 199062504 425545790 245523433 53437284 339065644 389386002 278770926 ... 375075216 452332390 259934779 55862550 361010972 412168035 292805460 ... 396657807

You can create an opportunity matrix from the reference genome using the method

genOpportunityFromGenome

from signeR package. See the documentation 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

rvalieris/signeR documentation built on April 20, 2024, 2:08 p.m.