needs library(Rgraphviz)

[jielab]

Hi, guys:

First, Happy New Year!

for the example code, the last step of visualization needs to load library(Rgraphviz) first. Otherwise, it won't work. So, it would be great to add "library(Rgraphviz)" to the example code, in case others run into the same problem.

BTW, what is the difference between TreeWAS and TreeWASDir ? Do I need to use both?

Best regards,
jie

[jielab]

Hi, there:

Happy New Year!

I was able to replicate the example code posted at Github, and got a figure like below.

It seems that rs4420638 are negatively associated with a lot of ICD-10 codes (blue color, State: -1), and positively associated with liver traits (red color, State: 1).

I thought that the "HES.data" used in the sample code should be a data frame with sample IDs and the corresponding ICD-10 codes for each sample. Instead, it is a data frame for SNP and lBF values. How to get this HES.data data frame is not clear to me. It would be great if you could expand this example code so that users could fully understand the process step by step.

I am also wondering how the TreeWAS analysis could be performed, because there are no "controls". It seems to me that all samples are "cases", with one of more ICD-10 codes for each sample, correct?

Thank you very much & best regards,
Jie