marouenbg
commented
6 months ago Hi @wilsonavac ,
if the input to MONSTER is a GRN, it has to be in TF-by-Gene format, I clarified the docs a bit here https://github.com/netZoo/netZooR/pull/312/files
Marouen
.Rmd = copd_smoking_feature_grn.Rmd line 293
MONSTER wrapper to input PANDA Results
domonster <- function(exp_graph, control_graph){ combdf <- as.data.frame(cbind(control_graph, exp_graph)) combdes <- c(rep(0, ncol(control_graph)),rep(1, ncol(exp_graph))) res <- monster(expr = combdf, design = combdes, motif = NA, nullPerms = 1, numMaxCores = 1, mode = 'regNet') return(res) }
Inputs
I checked inputs for Inf, NA, and Nan values and they were not present
y_cp_grn = read.table("/home/rstudio/copdgene_yes_cp_dev_panda.txt",sep=" ", header=T) n_cp_grn = read.table("/home/rstudio/copdgene_no_cp_dev_panda.txt",sep=" ", header=T)
Run MONSTER
ynmonster = domonster(y_cp_grn, n_cp_grn)
error
NAs introduced by coercionError in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in 'y'