Perturbations

A drug perturbation is defined as a single or a list of multiple drugs that are used upon a cell system. The perturbations file is a simple file where we write each perturbation in a different line. The drugs listed in a perturbation are separated by tabs. For example, having the four drugs A,B,C,D at our (computational) disposal, we can test the following perturbations using Drabme:

A
B
C
D
A   B
A   C
C   D
A   D
A   C   D

For every higher-order perturbation we want to test, the file must include the drug subsets in the order they are specified in the perturbation.

For example, to include the A,B,C perturbation (we use commas instead of tabs here) in the example file above, the subsets A,B, A,C and B,C must be also present before (the last is not). And by saying that order matters, we mean that writing C,B instead of B,C before the A,B,C perturbation, will generate an error. If a user wants to avoid such errors, then he must not specify a pertubations file in Drabme’s input files. What happens then, is that the drugs listed in the drug panel are used to generate all possible perturbations up to the number specified in Drabme’s configuration.