Merge branch 'devel'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: genefu
 Type: Package
 Title: Computation of Gene Expression-Based Signatures in Breast Cancer
-Version: 2.25.1
-Date: 2021-05-21
+Version: 2.39.1
+Date: 2021-11-27
 Authors@R: c(
   person('Deena M.A. Gendoo', role='aut'), 
   person('Natchar Ratanasirigulchai', role='aut'), 
@@ -12,6 +12,7 @@ Authors@R: c(
   person('Aleix Prat', role='aut'),
   person('Nikta Feizi', role='ctb'),
   person('Christopher Eeles', role='ctb'),
+  person('Jermiah Joseph', role='ctb'),
   person('Benjamin Haibe-Kains', email='[email protected]',
     role=c('aut', 'cre')))
 Description: This package contains functions implementing various tasks usually 
@@ -25,9 +26,9 @@ Depends: R (>= 4.1), survcomp, biomaRt, iC10, AIMS
 Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, 
   breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, 
   knitr, caret, survival, BiocStyle, magick, rmarkdown
-Imports: amap, impute, mclust, limma, graphics, stats, utils
+Imports: amap, impute, mclust, limma, graphics, stats, utils, iC10TrainingData
 VignetteBuilder: knitr
 License: Artistic-2.0
 Encoding: UTF-8
 URL: http://www.pmgenomics.ca/bhklab/software/genefu
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -51,6 +51,7 @@ export(tbrm)
 export(weighted.meanvar)
 export(write.m.file)
 import(graphics)
+import(iC10TrainingData)
 import(limma)
 import(mclust)
 import(stats)

R/molecular.subtyping.R

@@ -89,6 +89,7 @@ if(getRversion() >= "2.15.1")
 #' @examples
 #' ##### without mapping (affy hgu133a or plus2 only)
 #' # load VDX data
+#' require(iC10TrainingData)
 #' data(vdxs)
 #' data(AIMSmodel)
 #' data(scmgene.robust)
@@ -128,6 +129,7 @@ if(getRversion() >= "2.15.1")
 #'   annot=annot.vdxs, do.mapping=TRUE)
 #' table(sbt.vdxs.CL$subtype)
 #'
+#'
 #' @md
 #' @export
 molecular.subtyping <- function(sbt.model=c("scmgene", "scmod1", "scmod2",

R/package.R

@@ -0,0 +1,3 @@
+#' @keywords internal
+#' @import iC10TrainingData
+"_PACKAGE"