Clarification with degMerge function

[Chengyao-Peng]

Hi,

First of all, thanks for developing this package! It makes visualising DEA results easier.

However, I've been having trouble to use the function, degMerge, to find similar patterns in two omics layers.

Specifically, from the documentation, I'm not sure about the format of the matrix in matrix_list and the metadata_list. I prepared a list of two data frames for both variable but received this error:

Error in matrixnorm_list[[base]] :
attempt to select less than one element in get1index

What could be the problem causing this error?

Also, what should be put as the "summarize" variable? I understand it as a variable to describe the source of omics layers in the metadata matrix but I might be completely wrong.

It would be very appreciated if you could clarify a bit more about this function and have some example code in the documentation.

Kind regards,
Chengyao

[lpantano]

Hi,

I missed this. The input should be the same matrix you use for degPattern in both analysis, and the same metadata. Then, for the cluster_list, you can use the element df of the output of degPatter. The list should be named.

Summarize means the same than in degPattern, is the column in the metadata of both analysis to combine. They should have the same values. It is the groups you are interested in.

I can work in an example, but I can't promise when. If you can share the data, happy to help with that. Thanks.