search

NKI-CCB / DISCOVER

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data
Apache License 2.0
27 stars 6 forks source link

Stratifying data #16

Closed FireHavvk closed 1 year ago

FireHavvk commented 2 years ago

Hi, I'm working on a study on genetic interactions within different types of paediatric acute leukaemia. I want to add different tumour types together, but have been unable to stratify the data per tumour type and than add together all the data into one big matrix. How did you go about stratifying the pan cancer data described in your paper?

Kind regards, Charlotte

scanisius commented 2 years ago

The option to stratify your analysis is available as an extra argument to the discover.matrix (in R) or DiscoverMatrix (in Python) function. This argument is called strata. To stratify, you pass a vector of length equal to the number of tumours in your mutation matrix where the values specify the stratum (in your case the tumour type) for the corresponding tumours.

The following R example code illustrates this using the BRCA.mut data included in the discover package.

subtypes <- sample(c("TYPE1", "TYPE2"), ncol(BRCA.mut), replace=TRUE)   # replace this by the actual tumour types
events <- discover.matrix(BRCA.mut, strata=subtypes)
scanisius commented 1 year ago

This issue has been inactive for a while now, so I am closing it. Please open a new issue if you are still experiencing problems with DISCOVER.