Update puma (#286)

* 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 puma examples

* fix puma examples

* update docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: netZooR
 Type: Package
 Title: Unified methods for the inference and analysis of gene regulatory networks
-Version: 1.3.25
+Version: 1.3.28
 Date: 2023-03-27
 Authors@R: c(person("Marouen", "Ben Guebila",
 			email = "benguebila@hsph.harvard.edu", role = c("aut","cre"), comment = c(ORCID = "0000-0001-5934-966X")),

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(TIGER)
+export(adj2el)
+export(adj2regulon)
 export(alpaca)
 export(alpacaCrane)
 export(alpacaExtractTopGenes)
@@ -15,6 +18,8 @@ export(craneUnipartite)
 export(createCondorObject)
 export(createPandaStyle)
 export(dragon)
+export(el2adj)
+export(el2regulon)
 export(elistToAdjMat)
 export(lioness)
 export(lionessPy)
@@ -36,6 +41,8 @@ export(pandaDiffEdges)
 export(pandaPy)
 export(pandaToAlpaca)
 export(pandaToCondorObject)
+export(prior.pp)
+export(puma)
 export(runEgret)
 export(sambar)
 export(sourcePPI)

R/PUMA.R

@@ -45,8 +45,9 @@
 #' "coopNet" is the cooperative network which is not updated for miRNAs
 #' @examples
 #' data(pandaToyData)
+#' mirs = c("AHR","AR","ARID3A","ARNT","BRCA1","CEBPA","CREB1","DDIT3")
 #' pumaRes <- puma(pandaToyData$motif,
-#'            pandaToyData$expression,NULL,hamming=.1,progress=TRUE)
+#'            pandaToyData$expression,NULL,mir_file=mirs,hamming=.1,progress=TRUE)
 #' @references
 #' Kuijjer, Marieke L., et al. "PUMA: PANDA using microRNA associations." Bioinformatics 36.18 (2020): 4765-4773.
 puma <- function(motif,expr=NULL,ppi=NULL,alpha=0.1,mir_file,hamming=0.001,
@@ -238,11 +239,11 @@ puma <- function(motif,expr=NULL,ppi=NULL,alpha=0.1,mir_file,hamming=0.001,
     rownames(tfCoopNetwork) <- tf.names
   }
 
-  if(mir_file != NULL){
+  if(!is.null(mir_file)){
     mirIndex = match(mir_file,tf.names)
     tfCoopNetwork[mirIndex,] = 0
     tfCoopNetwork[,mirIndex] = 0
-    seqs = seq(1, num.tfs*num.tfs, num.tfs+1)
+    seqs = seq(1, num.TFs*num.TFs, num.TFs+1)
     tfCoopNetwork[seqs] <- 1
     # tfCoopNetwork has now a diagonal of 1 and all entries are zeros 
     # for miRNA-miRNA interactions and TF-miRNA interactions
@@ -288,7 +289,7 @@ puma <- function(motif,expr=NULL,ppi=NULL,alpha=0.1,mir_file,hamming=0.001,
     geneCoreg=minusAlpha*geneCoreg + alpha*CoReg2
 
     #PUMA step to skip update of PPI matrix for miRNA interactions
-    seqs = seq(1, num.tfs*num.tfs, num.tfs+1)
+    seqs = seq(1, num.TFs*num.TFs, num.TFs+1)
     savediag = tfCoopNetwork[seqs] # save diagonal
     tfCoopNetwork[mirIndex,] <- TFCoopInit[mirIndex,]
     tfCoopNetwork[,mirIndex] <- TFCoopInit[,mirIndex]
@@ -422,4 +423,4 @@ prepResult <- function(zScale, output, regulatoryNetwork, geneCoreg, tfCoopNetwo
 }
 
 pandaObj <- setClass("panda", slots=c("regNet","coregNet","coopNet","numGenes","numTFs","numEdges"))
-setMethod("show","panda",function(object){print.panda(object)})
+setMethod("show","panda",function(object){print.panda(object)})

R/SPIDER.R

@@ -50,8 +50,8 @@
 #' pandaToyData$epifilter = pandaToyData$motif
 #' nind=floor(runif(5000, min=1, max=dim(pandaToyData$epifilter)[1]))
 #' pandaToyData$epifilter[nind,3] = 0
-#' #spiderRes <- spider(pandaToyData$motif,pandaToyData$expression,
-#' #                    pandaToyData$epifilter,pandaToyData$ppi,hamming=.1,progress=TRUE)
+#' spiderRes <- spider(pandaToyData$motif,pandaToyData$expression,
+#'                     pandaToyData$epifilter,pandaToyData$ppi,hamming=.1,progress=TRUE)
 #' @references
 #' Sonawane, Abhijeet Rajendra, et al. "Constructing gene regulatory networks using epigenetic data." npj Systems Biology and Applications 7.1 (2021): 1-13.
 spider <- function(motif,expr=NULL,epifilter=NULL,ppi=NULL,alpha=0.1,hamming=0.001,