Closed sandraleebatista closed 1 year ago
Hi @sandraleebatista ,
I don't think that the code snippet corresponds to what we have, here is what lioness in netZooR looks like: https://github.com/netZoo/netZooR/blob/master/R/LIONESS.R#L183 You can call it with network.inference.method == "pearson" for a correlation network.
Best, Marouen
Thank you. That helped fix the tutorial, this line specifically: cormat <- lioness(dat, network.inference.method ="pearson")
Hi @sandraleebatista , I think lioness returns a list of objects each containing single-sample networks (coexpression in your case) https://github.com/netZoo/netZooR/blob/master/R/LIONESS.R#L172
Hello, do you have any lioness sample code in R? I tried the tutorial here: https://github.com/kuijjerlab/lionessR
Specifically I cannot get the lioness function itself work. (Specifically this line: cormat <- lioness(dat,netFun) (had used correlation for the network) Error in if (class(expr) == "ExpressionSet") expr <- assayData(expr)[["exprs"]] : )
However it did not work and I am not sure if it is because I am using lioness in R from netZooR. I had installed netZooR using BiocManager. I am not sure if the API should be different or if there is any other documentation.
Thank you, Sandra