I have a question. I know that I can use the create_custom_window to provide a list of "parent/regulator" genes, such as TF, to reduce the calculation time for big datasets. I was wondering whether there is a way also to answer this other question: I have a list of genes, and I am interested to get a ranked list of genes that best predict the response of the genes in this set. In other words, pre-filter for child column/regulated genes instead of parents/regulators.
Biologically, I am interested to see if I can find genes that are not necessarily TFs but are regulating a set of well-known genes that play an active role under a treatment.
I tried to modify create_custom_window function and a few others but it seems that I am breaking some internal variables and my results are either "wrong" compared to the example provided in this repo or the program crashes.
Hi,
I have a question. I know that I can use the create_custom_window to provide a list of "parent/regulator" genes, such as TF, to reduce the calculation time for big datasets. I was wondering whether there is a way also to answer this other question: I have a list of genes, and I am interested to get a ranked list of genes that best predict the response of the genes in this set. In other words, pre-filter for child column/regulated genes instead of parents/regulators. Biologically, I am interested to see if I can find genes that are not necessarily TFs but are regulating a set of well-known genes that play an active role under a treatment.
I tried to modify create_custom_window function and a few others but it seems that I am breaking some internal variables and my results are either "wrong" compared to the example provided in this repo or the program crashes.
Thanks a lot.
Best, Armin