fixed a bug in getActivity_individual(): invalid class "ExpressionSet…

…" object: sampleNames differ between assayData and phenoData. This happened when a hyphen exists in colnames.

R/network_analysis.R

@@ -828,7 +828,7 @@ getActivity_individual <- function(input_eset,
   acs <- cal_Activity(target_list = target_list, cal_mat = exprs(input_eset), activity_method = activity_method, do.std = do.z_normalization)
 
   ## prepare activity eset
-  acs_mtx <- data.frame(acs)
+  acs_mtx <- data.frame(acs, check.names = FALSE)
   acs_mtx <- acs_mtx[!is.na(row.names(acs_mtx)),]
 
   if (any(is.na(acs_mtx))) {
@@ -837,6 +837,12 @@ getActivity_individual <- function(input_eset,
     cat('NAs were found in the activity matrix and have been replaced by the minimum value: ', min_v, '.\n')
   }
 
+  if (any(is.na(acs_mtx))) {
+    min_v <- min(acs_mtx, na.rm = T)
+    acs_mtx[is.na(acs_mtx)] <- min_v
+    cat('NAs were found in the activity matrix and have been replaced by the minimum value: ', min_v, '.\n')
+  }
+
   acs_pd <- Biobase::pData(input_eset)
   acs_pd <- acs_pd[colnames(acs_mtx),]