From 5fd77ce4362aa91dfd1a918c165dd2f5b149ba0c Mon Sep 17 00:00:00 2001
From: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: Mon, 6 Jan 2025 15:34:36 -0500
Subject: [PATCH] load diseaseCodes from TCGAutils

---
 R/setup_subtype_clonality.R        | 11 ++++++++---
 vignettes/subtypeHeterogeneity.Rmd |  3 ++-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/R/setup_subtype_clonality.R b/R/setup_subtype_clonality.R
index 8bcd874..9b35d77 100644
--- a/R/setup_subtype_clonality.R
+++ b/R/setup_subtype_clonality.R
@@ -7,8 +7,13 @@
 # 
 ############################################################
 
+## DATA LOAD
+dataenv <- new.env(parent = emptyenv())
+data("diseaseCodes", package = "TCGAutils", envir = dataenv)
+diseaseCodes <- dataenv[["diseaseCodes"]]
+
 ## SETUP
-ctypes <- TCGAutils::diseaseCodes[,"Study.Abbreviation"]
+ctypes <- diseaseCodes[,"Study.Abbreviation"]
 
 ## cancer types
 .isSubClonal <- function(x) as.integer(x$Subclonal_HSCN_a1 | x$Subclonal_HSCN_a2)
@@ -56,7 +61,7 @@ ctypes <- TCGAutils::diseaseCodes[,"Study.Abbreviation"]
 
 ## GISTIC
 # @returns: a RangedSummarizedExperiment
-gistic2RSE <- function(ctype=TCGAutils::diseaseCodes[,"Study.Abbreviation"], 
+gistic2RSE <- function(ctype=ctypes,
     peak=c("wide", "narrow", "full"), cache=TRUE)
 {
     ctype <- match.arg(ctype)
@@ -141,7 +146,7 @@ gistic2RSE <- function(ctype=TCGAutils::diseaseCodes[,"Study.Abbreviation"],
 
 ## Broad subtypes
 # @returns: a matrix with sample IDs as rownames and at least a column "cluster"
-getBroadSubtypes <- function(ctype=TCGAutils::diseaseCodes[,"Study.Abbreviation"], 
+getBroadSubtypes <- function(ctype=ctypes,
     clust.alg=c("CNMF", "Consensus_Plus"), cache=TRUE)
 {
     ctype <- match.arg(ctype)
diff --git a/vignettes/subtypeHeterogeneity.Rmd b/vignettes/subtypeHeterogeneity.Rmd
index 409601a..251d9a6 100644
--- a/vignettes/subtypeHeterogeneity.Rmd
+++ b/vignettes/subtypeHeterogeneity.Rmd
@@ -63,7 +63,8 @@ names(stcols) <- SUBTYPES
 
 ## Cancer types
 ```{r ctypes}
-TCGAutils::diseaseCodes[,c("Study.Abbreviation", "Study.Name")]
+data("diseaseCodes", package = "TCGAutils")
+diseaseCodes[,c("Study.Abbreviation", "Study.Name")]
 ```
 
 ## ABSOLUTE