renaming

BASALT.Rproj

@@ -0,0 +1,21 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette

DESCRIPTION

@@ -1,10 +1,10 @@
-Package: BASAL
+Package: BASALT
 Type: Package
-Title: What the Package Does (Title Case)
+Title: Breast Cancer Subtype Analysis Tool
 Version: 0.1
 Date: 2015-07-08
-Author: Who wrote it
-Maintainer: Who to complain to <[email protected]>
-Description: More about what it does (maybe more than one line)
-License: What license is it under?
-LazyData: TRUE
+Author: Ben Elsworth
+Maintainer: <[email protected]>
+Description: Breast Cancer Subtype Analysis
+License: None
+LazyData: TRUE

R/pam50_correlation_plot.R

@@ -40,6 +40,7 @@ multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
 #' @param p50 The PAM50 results text file
 #' @param id The ID of the samples to extract
 #' @param name The name to represent the samples
+#' @param outDir The output directory
 cor_plot = function(p,id,name,outDir){
   print(paste0("Generating correlation plots - ",id," - ",name))
   p$X=rownames(p)
@@ -90,5 +91,3 @@ cor_plot = function(p,id,name,outDir){
   multiplot(p1,p2,cols=2)
   dev.off()
 }
-
-#cor_plot(p50_res,".","name")