inst/extdata/snv_help.md

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

SNV matrix

SNV matrix is a text file with a (tab-delimited) matrix of SNV counts found on analyzed genomes. It must contain one row for each genome sample and 97 columns, the first one with sample IDs and, after that, one column for each mutation type. Mutations should be specified in the column names (headers), by both the base change and the trinucleotide context where it occurs (for example: C>A:ACA). The table below shows an example of the SNV matrix structure.

C>A:ACA C>A:ACC C>A:ACG C>A:ACT C>A:CCA ... T>G:TTT PD3851a 31 34 9 21 24 ... 21 PD3904a 110 91 9 87 108 ... 77 ... ... ... ... ... ... ... ... PD3890a 122 112 13 107 99 ... 50

You can create an SNV matrix from a VCF file using the method

genCountMatrixFromVcf

or from a MAF file using the method

genCountMatrixFromMAF

from signeR package. See the documentation for more details.

Columns

The first column needs to contain the sample ID and the other columns contain the 96 trinucleotide contexts.

Rows

Each row contains the sample ID and the counts for each trinucleotide context.

Example file

21 breast cancer

VCF example

MAF example

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