Behind the scenes

This section will point out some parts which might be interesting if you are running OncodriveFML yourself.

Command line interface

The command line interface of OncodriveFML overwrites some of the parameters in the configuration file.

Warning

This overwrite is performed regardless the parameter is set or not in the configuration file.

The flag --no-indels also affects the indels configuration parameters. Particularly, it has effect on the include option. The use of this flag discards the analysis of indels by setting include = False.

Using the --signature of the command line, set the signature configuration to method = "file" and path = "<provided path>"

Note

Signatures provided as an external file are not normalized.

The table below shows the effects of the --signature-correction flag in the signature configuration:

Effects of –signature-correction

Value	Effect in signature
wg	normalize_by_sites = 'whole_genome'
wx	normalize_by_sites = 'whole_exome'

Note

This option does not have any impact if signatures are passed with the --signature option.

BgData

OncodriveFML uses external data retrieved using the BgData package. You can download and check this data yourself. If you want to use different data, you can download the source code and modify the code to use your own data.

Reference genome

As March 2017 BgData includes three reference genomes: HG18, HG19 and HG38.

bgdata datasets/genomereference/hg38

If you want to use a different genome, you need to modify the code in the oncodrivefml.signature module.

Gene stops

OncodriveFML also uses a tabix file that contains the positions and the alterations of the gene stops.

bgdata datasets/genestops/hg38