Option for male/femal

NAMESPACE

@@ -98,5 +98,6 @@ export(widen_bins)
 export(widen_haplotypebins)
 import(data.table)
 importFrom(Rcpp,sourceCpp)
+importFrom(data.table,":=")
 importFrom(magrittr,"%>%")
 useDynLib(signals)

R/callHSCN.R

@@ -634,6 +634,7 @@ filter_haplotypes <- function(haplotypes, fraction){
 #' @param fillmissing For bins with missing counts fill in values based on neighbouring bins
 #' @param global_phasing_for_diploid When using cluster_per_chr, use all cells for phasing diploid regions within the cluster
 #' @param chrs_for_global_phasing Which chromosomes to phase using all cells for diploid regions, default is NULL which uses all chromosomes
+#' @param female Default is `TRUE`, if set to `FALSE` and patient is "XY", X chromosome states are set to A|0 where A=Hmmcopy state
 #' 
 #' @return Haplotype specific copy number object 
 #' 
@@ -691,7 +692,8 @@ callHaplotypeSpecificCN <- function(CNbins,
                                     smoothsingletons = TRUE,
                                     fillmissing = TRUE,
                                     global_phasing_for_balanced = FALSE,
-                                    chrs_for_global_phasing = NULL) {
+                                    chrs_for_global_phasing = NULL,
+                                    female = TRUE) {
   if (!clustering_method %in% c("copy", "breakpoints")) {
     stop("Clustering method must be one of copy or breakpoints")
   }
@@ -720,6 +722,17 @@ callHaplotypeSpecificCN <- function(CNbins,
     haplotypes$chr <- sub("chr", "", haplotypes$chr)
   }
 
+  if (female == TRUE){
+    #do not infer states for chr "Y"
+    haplotypes <- filter(haplotypes, chr != "Y")
+    CNbins <- filter(CNbins, chr != "Y")
+  } else{
+    #do not infer states for chr "X" or "Y"
+    haplotypes <- filter(haplotypes, chr != "Y")
+    haplotypes <- filter(haplotypes, chr != "X")
+    CNbins <- filter(CNbins, chr != "Y")
+  }
+
   nhaplotypes <- haplotypes %>% 
     dplyr::group_by(cell_id) %>% 
     dplyr::summarize(n = sum(totalcounts)) %>% 
@@ -927,6 +940,12 @@ callHaplotypeSpecificCN <- function(CNbins,
     out[["data"]] <- out[["data"]] %>% 
       dplyr::mutate(A = ifelse(state == 0, 0, A)) %>% 
       dplyr::mutate(B = ifelse(state == 0, 0, B))
+    if (female == FALSE){
+      #for male patients set A == state and B == 0
+      out[["data"]] <- out[["data"]] %>% 
+        dplyr::mutate(A = ifelse(chr == "X", state, A)) %>% 
+        dplyr::mutate(B = ifelse(chr == "X", 0, B))
+    }
     out[["data"]] <- add_states(out[["data"]])
     out[["data"]] <- as.data.frame(out[["data"]])
   }

R/clustering.R

@@ -92,7 +92,8 @@ umap_clustering <- function(CNbins,
                                 ret_model = TRUE,
                                 ret_nn = TRUE,
                                 pca = pca,
-                                fast_sgd = fast_sgd)
+                                fast_sgd = fast_sgd,
+                                pca_method = "svdr")
     }
   )