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Frequently Asked Questions

Which are the input file formats?

Check out the documentation to find information about the formats of the files: http://oncodrivefml.readthedocs.io/en/2.0.3/files.html.

Where can I get the source code to run OncodriveFML?

You can get the source code and install OncodriveFML from our git repository.

OncodriveFML stable releases are tagged. We recommend to download the latest stable release. If you prefer to have the latest code, you can clone and install the repository, however we cannot guarantee that it will work. The version that corresponds to the paper is 1.0.

Is there documentation for OncodriveFML?

Yes, the documentation is published on Read The Docs. Please, make sure that the documentation you get corresponds to the version you are using. For versions of OncodriveFML prior to 2.0 check the README files in our git repository.

Is it possible to do a more customized analysis with OncodriveFML?

Yes, web application has limited configuration capabilities. Install OncodriveFML and check all the parameters that can be configured in the configuration file.

What are the different parameters and what do they mean?

The most important parameters are the mutations file and the genomic elements file. The first one is referred in the REST API as input as well as in the OncodriveFML command line interface. The genomic elements file, named as elements in the REST API contains the genomic elements that OncodriveFML will analyse. While in the REST API it is required to submit a file in the web application you can also choose between some precomputed genomic regions.

If you upload you own genomic elements file, you also need to provide its type (type parameter in the REST API). The type indicates OncodriveFML if the regions under analysis are coding or noncoding regions. The sequencing parameter indicates how the mutations file was obtainded. The different parameters are:

wgs
Whole genome
wes
Whole exome
targeted
Targeted sequencing

If you do not know, use targeted. The indels parameter is a flag indicating whether to use or not indels in the analysis. As it is a flag, if it is present in the request then indels are used. If missing, indels are discarded.

These parameters can also be found in the command line interface of OncodriveFML (indels is replaced by the --no-indels flag, with the opposite behaviour).

Check OncodriveFML documentation to see how these parameters affect the analysis.

The scores parameters indicates which scores to use in the analysis. The options are:

cadd1.0
CADD v1.0
cadd1.3
CADD v1.3

The signature indicates which signature to use. Options are:

full
Compute signature by cancer type
bysample
Compute signature by sample
none
Do not use any signature
If you are doubting, you can read the OncodriveFML documentation and have a look at this page.

The different statistical methods that are supported by OncodriveFML are:

amean
Arithmetic mean
gmean
Geometric mean

Which signature should I use?

The signature represents the probability of a certain substitution to occur within its context. OncodriveFML computes the signature using the whole dataset, grouping the mutations by the category on the datasets columns CANCER_TYPE or SAMPLE. You can also choose to not use any signature. Find more information in the OncodriveFML documentation.

Is there a REST API?

No, we are not supporting the REST endpoint. If you want to use OncodriveFML programatically, please intall OncodriveFML in your machine. The code, as well as installation instructions, can be found in our git repository.