makeNetworks added

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(installPyDependencies)
+export(makeNetworks)
 export(manifoldAlignment)
 export(pcNet)
 export(tensorDecomposition)

R/makeNetworks.R

@@ -0,0 +1,17 @@
+#' @export makeNetworks
+#' @importFrom Matrix Matrix
+makeNetworks <- function(X, nNet = 10, nCells = 1000, nComp = 3, scaleScores = TRUE, symmetric = FALSE, q = 0.95){
+  sapply(seq_len(nNet), function(W){
+    Z <- sample(x = colnames(X), size = nCells, replace = TRUE)
+    Z <- as.matrix(X[,Z])
+    Z <- Z[apply(Z,1,sum) > 0,]
+    Z <- pcNet(Z, nCom = nComp, scaleScores = scaleScores, symmetric = symmetric, q = q)
+    geneList <- rownames(X)
+    nGenes <-length(geneList)
+    O <- matrix(data = 0, nrow = nGenes, ncol = nGenes)
+    rownames(O) <- colnames(O) <- geneList
+    O[rownames(Z), colnames(Z)] <- as.matrix(Z)
+    O <- Matrix::Matrix(O)
+    return(O)
+  })
+}