From ef745529237f99608f8b2dddc6f5e769f15a58c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Manuel=20Padr=C3=B3n=20Mart=C3=ADnez?= Date: Sat, 5 Nov 2022 15:03:32 +0000 Subject: [PATCH 1/2] Common code extraction --- R/CoRe.R | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/R/CoRe.R b/R/CoRe.R index 057f2a2..f020e71 100644 --- a/R/CoRe.R +++ b/R/CoRe.R @@ -54,13 +54,7 @@ CoRe.Binarize_Matrix<-function(depMat, names(FC) <- rownames(depMat) -FDR_Threshold(FC,ess_genes,noness_genes,FDRth=FDRth) }) - - bdep <- matrix(0, ncol = ncol(depMat), nrow = nrow(depMat), dimnames = dimnames(depMat)) - - for (i in 1:ncol(depMat)){ - bdep[which(depMat[,i] < sig_thrs[i]),i] <- 1 - } - + } else { if (scaled){ depMat<-CoRe.scale_to_essentials(depMat, ess_genes, noness_genes) @@ -79,14 +73,14 @@ CoRe.Binarize_Matrix<-function(depMat, } sig_thrs <- rep(threshold, ncol(depMat)) } + } - bdep <- matrix(0, ncol = ncol(depMat), nrow = nrow(depMat), dimnames = dimnames(depMat)) + bdep <- matrix(0, ncol = ncol(depMat), nrow = nrow(depMat), dimnames = dimnames(depMat)) - for (i in 1:ncol(depMat)){ - bdep[which(depMat[,i] < sig_thrs[i]),i] <- 1 - } + for (i in 1:ncol(depMat)){ + bdep[which(depMat[,i] < sig_thrs[i]),i] <- 1 } - + return(bdep) } From c7f4a0ae062928e1a42f9adf5a55d3ece62c3758 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Manuel=20Padr=C3=B3n=20Mart=C3=ADnez?= Date: Sat, 5 Nov 2022 15:05:03 +0000 Subject: [PATCH 2/2] Using R syntax is faster than for loop --- R/CoRe.R | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/R/CoRe.R b/R/CoRe.R index f020e71..8e7706a 100644 --- a/R/CoRe.R +++ b/R/CoRe.R @@ -77,10 +77,7 @@ CoRe.Binarize_Matrix<-function(depMat, bdep <- matrix(0, ncol = ncol(depMat), nrow = nrow(depMat), dimnames = dimnames(depMat)) - for (i in 1:ncol(depMat)){ - bdep[which(depMat[,i] < sig_thrs[i]),i] <- 1 - } - + bdep[,] <- as.integer(depMat[,] < sig_thrs[]) return(bdep) }