Merge pull request #10 from ncborcherding/main

Reproducible eplet and creg internal data

Author: ncborcherding

NAMESPACE

@@ -13,9 +13,13 @@ export(plotSAB)
 export(quantifyEpletMismatch)
 export(quantifyMismatch)
 export(serologyAUC)
+export(spiDeconvolute)
 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)
@@ -71,6 +75,8 @@ importFrom(pracma,trapz)
 importFrom(purrr,map2_chr)
 importFrom(purrr,map_dfr)
 importFrom(readxl,read_excel)
+importFrom(stats,mad)
+importFrom(stats,median)
 importFrom(stringr,str_c)
 importFrom(stringr,str_extract)
 importFrom(tibble,as_tibble)
@@ -84,13 +90,5 @@ importFrom(treemapify,geom_treemap_text)
 importFrom(utils,data)
 importFrom(utils,globalVariables)
 importFrom(utils,head)
-importFrom(utils,read.csv)
-export(spiDeconvolute)
-importFrom(data.table,as.data.table)
-importFrom(data.table,copy)
-importFrom(data.table,dcast)
-importFrom(data.table,fcase)
-importFrom(data.table,rbindlist)
-importFrom(stats,mad)
-importFrom(stats,median)
 importFrom(utils,modifyList)
+importFrom(utils,read.csv)

R/calculateAuc.R

@@ -72,9 +72,9 @@ calculateAUC <- function(result_file,
     )
   } else if (tolower(analysis_type) == "creg") {
     config <- list(
-      feature_col = "creg",
+      feature_col = "CREG",
       data = deepMatchR::deepMatchR_cregs,
-      default_group_by = "creg"
+      default_group_by = "CREG"
     )
   } else if (tolower(analysis_type) == "serology") {
     config <- list(

R/cregAuc.R

@@ -360,12 +360,4 @@ if(getRversion() >= "2.15.1") {
   ]
 
   return(sorted_levels)
-}
-
-#' @importFrom keras3 load_model
-.loadModel <- function(chain, class) {
-  select  <- system.file("extdata", paste0(class, "_encoder.keras"), 
-                         package = "deepMatchR")
-  model <- load_model(select, compile = FALSE)
-  return(model)
-}
+}