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
, while not using it
includes indels (include = True
).
The table below shows the effects of the --sequencing flag in the signature configuration:
Value | Effect in signature |
---|---|
wgs | normalize_by_sites = 'whole_genome' |
wes | normalize_by_sites = 'whole_exome' |
targeted | normalize_by_sites = None |
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.
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 hg19
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 hg19