Merge pull request #15 from ncborcherding/main

Fixing issues with epletLoad and toSerology

Author: ncborcherding

NAMESPACE

@@ -22,7 +22,6 @@ export(predictMHCnuggets)
 export(quantifyEpletMismatch)
 export(quantifyMismatch)
 export(serologyAUC)
-export(spiDeconvolute)
 export(toSerology)
 export(updateWmdaData)
 export(visualizePeptideBinding)
@@ -31,10 +30,7 @@ importFrom(basilisk,basiliskStart)
 importFrom(basilisk,basiliskStop)
 importFrom(data.table,`:=`)
 importFrom(data.table,as.data.table)
-importFrom(data.table,copy)
 importFrom(data.table,data.table)
-importFrom(data.table,dcast)
-importFrom(data.table,fcase)
 importFrom(data.table,fifelse)
 importFrom(data.table,rbindlist)
 importFrom(data.table,set)
@@ -85,13 +81,10 @@ importFrom(readxl,read_excel)
 importFrom(reticulate,import)
 importFrom(reticulate,py_run_string)
 importFrom(stats,as.formula)
-importFrom(stats,mad)
-importFrom(stats,median)
 importFrom(stats,reorder)
 importFrom(stats,setNames)
 importFrom(stats,xtabs)
 importFrom(utils,data)
 importFrom(utils,globalVariables)
 importFrom(utils,head)
-importFrom(utils,modifyList)
 importFrom(utils,read.csv)

R/calculateEpletLoad.R

@@ -106,22 +106,27 @@ calculateEpletLoad <- function(recipient_geno,
   )
   names(eplet_sets) <- all_alleles
 
-  # Helper: donor-specific eplet count for one pair
+  # Helper: donor-specific eplet count for one pair (used for pairwise matrix)
   pair_count <- function(rec_a, don_a) {
     if (identical(rec_a, don_a)) return(0L)
     rec_set <- eplet_sets[[rec_a]]
     don_set <- eplet_sets[[don_a]]
     length(setdiff(don_set, rec_set))
   }
-  
-  # Helper: total per locus
+
+ # Helper: total per locus - uses union of all recipient allele eplets vs union of all donor allele eplets
   locus_total <- function(L) {
     rL <- r_alleles[grep(paste0("^", L, "_"), names(r_alleles))]
     dL <- d_alleles[grep(paste0("^", L, "_"), names(d_alleles))]
     if (length(rL) == 0L || length(dL) == 0L) return(0L)
-    total <- 0L
-    for (ra in rL) for (da in dL) total <- total + pair_count(ra, da)
-    total
+
+    # Union of all recipient eplets at this locus
+    rec_union <- unique(unlist(eplet_sets[rL], use.names = FALSE))
+    # Union of all donor eplets at this locus
+    don_union <- unique(unlist(eplet_sets[dL], use.names = FALSE))
+
+    # Count donor-specific eplets (in donor but not in recipient)
+    length(setdiff(don_union, rec_union))
   }
 
   if (return == "total") {