Filtering genes in IMAT #28
Description
IMAT should only use genes that appear in both the dataset and the model, similar to MADE.
As reported by a user:
I did encounter a small problem with the toolbox a few days ago, though it is actually more a result of improper use than a fault in the script, however I thought it might be something you would want to know.
I had a cobra model where I changed the gene association for a certain reaction, as a side-effect, this resulted in a set of genes now no longer associated with any reactions. After using the cobra_to_tiger function, only those genes which are associated in a reaction are put in tiger.varnames. This however results in a problem when running iMAT:
imat -> add_diff -> convert_ids:
Some indexes end up being 0 which give a problem in add_diff, as an index has to be a positive integer or logical...
- Bitbucket: https://bitbucket.org/csbl/tiger/issue/29
- Originally reported by: Paul Jensen
- Originally created at: 2012-08-15T00:19:47.285