fix main function

kalidouBA · Dec 11, 2023 · e9c50a1 · e9c50a1
1 parent 6cccfe4
commit e9c50a1
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Showing 2 changed files with 6 additions and 11 deletions.
diff --git a/R/DICEPRO.R b/R/DICEPRO.R
@@ -72,21 +72,16 @@ DICEPRO <- function(reference, bulk, methodDeconv = "CSx", cibersortx_email = NU
   bulk <- as.data.frame(apply(bulk[geneIntersect, ], 2, as.numeric))
   rownames(reference) <- rownames(bulk) <- geneIntersect
 
-  matrixAbundances <- performs <- normFrobs <- performs2plot <- opt <- NULL
+  out_Dec <- running_method(bulk, reference, methodDeconv, cibersortx_email, cibersortx_token)
+  k_CT <- ncol(reference) + 1
 
-  out_Dec <- running_method(bulk, W, methodDeconv, cibersortx_email, cibersortx_token)
-  B_Deconv <- as.matrix(W) %*% t(out_Dec)
-
-  k_CT <- ncol(W)
-
-  res <- nmf_conjugate_gradient(V = bulk, W = W, H = out_Dec, k_CT+1)
+  res <- nmf_conjugate_gradient(V = bulk, W = reference, H = out_Dec, k = k_CT)
   W <- res$W
 
-  colnames(W) <- c(cellTypeName, paste0("Unknown"))
+  dimnames(W) <- list(geneIntersect, c(cellTypeName, paste0("Unknown")))
 
-  out_Dec_Update <- res$H[,1:ncol(out_Dec)]
+  out_Dec_Update <- res$H[,-k_CT]
   dimnames(out_Dec_Update) <- dimnames(out_Dec)
-  rownames(performs2plot) <- NULL
 
   results <- list("Prediction" = out_Dec_Update, "New_signature" = W)
 

diff --git a/R/NMF_optim.R b/R/NMF_optim.R
@@ -64,7 +64,7 @@ nmf_conjugate_gradient <- function(V, k = 1, W = NULL, H = NULL) {
 
     list(W = W, H = t(H), Error = rmse_nmf)
   }
- cl <-  min(5, detectCores())
+  cl <-  min(5, detectCores())
   result_list <- mclapply(seq(0,1,0.25), function(i) {
     par_nmf(i)
   }, mc.cores = cl)