inst/extdata/knownsigs_help.md

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

Previous signatures matrix

Previous signatures is a tab-delimited text file with a matrix of previously known signatures. It must contain one column for each signature and one row for each of the 96 SNV types (considering trinucleotide contexts). Mutation types should be contained in the first column, in the same form as the column names of the SNV matrix. The table below shows an example of the previous signatures matrix structure.

Signature 2 Signature 3 Signature 5 Signature 6 ... Signature 8 C>A:ACA 0.01110 0.00067 0.02218 0.01494 ... 0.03672 C>A:ACC 0.00915 0.00062 0.01788 0.00896 ... 0.03324 C>A:ACG 0.00150 0.00010 0.00213 0.00221 ... 0.00252 ... ... ... ... ... ... ... T>G:TTT 0.00403 2.359E-05 0.0130 0.01337 ... 0.00722

Columns

The first column needs to contain the trinucleotide contexts and the other columns contain the known signatures.

Rows

Each row contains the expected frequency of the given mutation in the appointed trinucleotide context.

Example file

21 breast cancer

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