Fix 309 (#310)

* update documentation

* remove monster tests

* reduce monstr test

* update documentation

* remove diffedge example

* reduce monster tests

* remove spider example

* update monster examples

* remove lioness tests

* remove pada tests

* add citation

* fix 309

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: netZooR
 Type: Package
 Title: Unified methods for the inference and analysis of gene regulatory networks
-Version: 1.5.4
-Date: 2023-09-25
+Version: 1.5.6
+Date: 2024-02-02
 Authors@R: c(person("Marouen", "Ben Guebila",
 			email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),
 	     person("Tian", "Wang", 

R/PUMA.R

@@ -89,7 +89,11 @@ puma <- function(motif,expr=NULL,ppi=NULL,alpha=0.1,mir_file,hamming=0.001,
       expr <- expr[order(rownames(expr)),]
     }else if(mode=='union'){
       gene.names=unique(union(rownames(expr),unique(motif[,2])))
-      tf.names  =unique(union(unique(ppi[,1]),unique(motif[,1])))
+      if(is.null(ppi)){
+        tf.names  = unique(motif[,1])        
+      }else{
+        tf.names  =unique(union(unique(ppi[,1]),unique(motif[,1])))
+      }
       num.TFs    <- length(tf.names)
       num.genes  <- length(gene.names)
       # gene expression matrix
@@ -117,7 +121,11 @@ puma <- function(motif,expr=NULL,ppi=NULL,alpha=0.1,mir_file,hamming=0.001,
       regulatoryNetwork[Idx]=motif[,3]
     }else if(mode=='intersection'){
       gene.names=unique(intersect(rownames(expr),unique(motif[,2])))
-      tf.names  =unique(intersect(unique(ppi[,1]),unique(motif[,1])))
+      if(is.null(ppi)){
+        tf.names  =unique(motif[,1])       
+      }else{
+        tf.names  =unique(intersect(unique(ppi[,1]),unique(motif[,1])))
+      }
       num.TFs    <- length(tf.names)
       num.genes  <- length(gene.names)
       # gene expression matrix
@@ -241,6 +249,7 @@ puma <- function(motif,expr=NULL,ppi=NULL,alpha=0.1,mir_file,hamming=0.001,
 
   if(!is.null(mir_file)){
     mirIndex = match(mir_file,tf.names)
+    mirIndex <- mirIndex[!is.na(mirIndex)]
     tfCoopNetwork[mirIndex,] = 0
     tfCoopNetwork[,mirIndex] = 0
     seqs = seq(1, num.TFs*num.TFs, num.TFs+1)