Merge pull request #8 from gabrielgesteira/diploid_fix

Revert Pgametes and Qgametes change
gabrielgesteira · Mar 20, 2024 · 2578b35 · 2578b35
2 parents 5c9ec33 + 458038e
commit 2578b35
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/R/read_data.R b/R/read_data.R
@@ -115,13 +115,13 @@ read_data <- function(ploidy = 6, geno.prob, geno.dose = NULL, double.reduction
     Palleles <- letters[1:ploidy]; length(Palleles)
     Pgametes <- gtools::combinations(length(Palleles), ploidy/2, Palleles, repeats.allowed = TRUE); dim(Pgametes)
     Punique <- apply(Pgametes, 1, unique); length(Punique)
-    Pgametes <- apply(Pgametes[which(lapply(Punique, length) >= n.unique),], 1, paste, collapse=""); length(Pgametes)
-    # Pgametes <- lapply(combn(Palleles, ploidy/2, simplify = FALSE), paste, collapse=""); length(Pgametes)
+    ## Pgametes <- apply(Pgametes[which(lapply(Punique, length) >= n.unique),], 1, paste, collapse=""); length(Pgametes)
+    Pgametes <- lapply(combn(Palleles, ploidy/2, simplify = FALSE), paste, collapse=""); length(Pgametes)
     Qalleles <- letters[(ploidy+1):(2*ploidy)]
     Qgametes <- gtools::combinations(length(Qalleles), ploidy/2, Qalleles, repeats.allowed = TRUE); dim(Qgametes)
     Qunique <- apply(Qgametes, 1, unique); length(Qunique)
-    Qgametes <- apply(Qgametes[which(lapply(Qunique, length) >= n.unique),], 1, paste, collapse=""); length(Qgametes)
-    # Qgametes <- lapply(combn(Qalleles, ploidy/2, simplify = FALSE), paste, collapse="")
+    ## Qgametes <- apply(Qgametes[which(lapply(Qunique, length) >= n.unique),], 1, paste, collapse=""); length(Qgametes)
+    Qgametes <- lapply(combn(Qalleles, ploidy/2, simplify = FALSE), paste, collapse="")
     genotypes <- as.vector(t(outer(Pgametes, Qgametes, paste, sep="")))
     sibs <- sapply( genotypes, FUN=function(x) paste(x, genotypes, sep="") )
     Pi <- matrix(data = NA, nrow = length(Pgametes)^2, ncol = length(Pgametes)^2)