diff --git a/DESCRIPTION b/DESCRIPTION index a912f76..4b5d103 100644 --- a/DESCRIPTION +++ b/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='benjamin.haibe.kains@utoronto.ca', 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 diff --git a/NAMESPACE b/NAMESPACE index c2d18b4..91f8851 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -51,6 +51,7 @@ export(tbrm) export(weighted.meanvar) export(write.m.file) import(graphics) +import(iC10TrainingData) import(limma) import(mclust) import(stats) diff --git a/R/molecular.subtyping.R b/R/molecular.subtyping.R index 812f948..97c30fd 100644 --- a/R/molecular.subtyping.R +++ b/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", diff --git a/R/package.R b/R/package.R new file mode 100644 index 0000000..6dff438 --- /dev/null +++ b/R/package.R @@ -0,0 +1,3 @@ +#' @keywords internal +#' @import iC10TrainingData +"_PACKAGE" \ No newline at end of file diff --git a/man/genefu-package.Rd b/man/genefu-package.Rd new file mode 100644 index 0000000..7d5e97b --- /dev/null +++ b/man/genefu-package.Rd @@ -0,0 +1,38 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/package.R +\docType{package} +\name{genefu-package} +\alias{genefu} +\alias{genefu-package} +\title{genefu: Computation of Gene Expression-Based Signatures in Breast Cancer} +\description{ +This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis. +} +\seealso{ +Useful links: +\itemize{ + \item \url{http://www.pmgenomics.ca/bhklab/software/genefu} +} + +} +\author{ +\strong{Maintainer}: Benjamin Haibe-Kains \email{benjamin.haibe.kains@utoronto.ca} + +Authors: +\itemize{ + \item Deena M.A. Gendoo + \item Natchar Ratanasirigulchai + \item Markus S. Schroeder + \item Laia Pare + \item Joel S Parker + \item Aleix Prat +} + +Other contributors: +\itemize{ + \item Nikta Feizi [contributor] + \item Christopher Eeles [contributor] +} + +} +\keyword{internal} diff --git a/man/molecular.subtyping.Rd b/man/molecular.subtyping.Rd index 7ed4f72..4d21bdb 100644 --- a/man/molecular.subtyping.Rd +++ b/man/molecular.subtyping.Rd @@ -41,6 +41,7 @@ Clustering Model fitted by subtype.cluster. \examples{ ##### without mapping (affy hgu133a or plus2 only) # load VDX data +require(iC10TrainingData) data(vdxs) data(AIMSmodel) data(scmgene.robust) @@ -80,6 +81,7 @@ sbt.vdxs.CL <- molecular.subtyping(sbt.model="claudinLow", data=data.vdxs, annot=annot.vdxs, do.mapping=TRUE) table(sbt.vdxs.CL$subtype) + } \references{ T. Sorlie and R. Tibshirani and J. Parker and T. Hastie and J. S. Marron and A.