CHANGES IN VERSION 1.3.93 (03 May 2016) ------------------------- rm \usepackage{zi4} CHANGES IN VERSION 1.3.91 (01 May 2016) ------------------------- rm canceR.pdf and lines from canceR.Rnw %\VignetteEngine{R.rsp::tex} %\VignetteKeyword{R} %\VignetteKeyword{package} %\VignetteKeyword{vignette} %\VignetteKeyword{LaTeX} %\VignetteAuthor{Karim Mezhoud} %\VignetteDepends{} %\VignetteKeywords{ A Graphical User Interface for accessing and modeling the MSKCC Cancer Genomics Data.} %\VignettePackage{canceR} CHANGES IN VERSION 1.3.7 (07 April 2016) ------------------------ add /extdata/canceR.pdf CHANGES IN VERSION 1.3.6 (05 April 2016) ------------------------ fix paths in running examples CHANGES IN VERSION 1.3.5 (04 April 2016) ------------------------ git reset --hard HEAD~ bash ../update_remotes.sh add vignette/image, pump version, delete canceR.tex git commit -m "fix vignette rm canceR.tex" git svn rebase git svn dcommit --add-author-from CHANGES IN VERSION 1.3.2 (28 Mars 2016) ------------------------ Bioc devel canceR is not updated to version 1.3.1 Just add image in README CHANGES IN VERSION 1.3.1 (24 Mars 2016) ------------------------ rewrite documents using roxygen rewrite test package include .travis check system CHANGES IN VERSION 1.1.2 (12 May 2015) ------------------------ 1- add Circos function to plot Menu Function 1: getGeneListmSigDB(): get Gene list and their gene Sets from MSigDB Function 1.1: dialoggetGeneListMSigDB(): Select Gene Sets from list and extract hem genes Function 2: getListProfData(): This function save Profiles Data of cancer in lists; Outputs:myGlobalEnv$ListProfData$Expression myGlobalEnv$ListProfData$CNA myGlobalEnv$ListMetData$HM450$StudiesRef myGlobalEnv$ListMetData$HM27$StudiesRef myGlobalEnv$ListProfData$RPPA$StudiesRef myGlobalEnv$ListProfData$miRNA$StudiesRef myGlobalEnv$ListMutData$StudiesRef myGlobalEnv$Freq_DfMutData Function 3 : getCircos(dimension="All"): Main fucntion of Circos plot: plot Tracks (dimensions) and Sectors (diseases) Function 3.1: getCor_ExpCNAMet(ListMatrix, dimension) Function 3.2: dialogOptionCircos(): specifing which dimension and Threshold gene dimensions levels will be plot. 1- dialogMetOption(): add "Circos" argument to make the difference between getMetDataMultipleGene() and getListMetData() 2- getGeneList(): add rm("GeneListMSigDB"", envir="myGlobalEnv") CHANGES IN VERSION 1.1.1 (27 April 2015) ------------------------ 1- Survival plot 1.1 add getSurvival(Coxph) and getSurvival.Rd file 1.1 getOptionGSEAlm(s, ClinicalData): add line 105 ### only for Survival plot myGlobalEnv$variable <- as.formula(sprintf("Surv(OS_MONTHS,OS_STATUS)~%s", coVariables)) 1.2 cancer.latex file: add Survival plot paragraph 1.3 add image in /image folder: KM.png, Coxph.png 1.4 getCasesGenProfs(): add getSurvival in Plot menu RELEASE 1.0.0 (17 April 2015) ------------------------- CHANGES IN VERSION 0.99.3 ------------------------- o getProfilesDataMultipleGenes: line 78: Test only Genetic Profiles having mRNA expression to get Profile Data. o getMutData(): line 96 change .GlobalEnv to myGlobalEnv) o getProfDataMultipleGenes(): line 7 add testCheckedCaseGenProf() CHANGES IN VERSION 0.99.2 ------------------------- o Add documentation for RUN.GSEA() function o Remove dependency of RSvgDevice. This package is not available for Windows OS. CHANGES IN VERSION 0.99.1 ------------------------- o Add examples in documents SIGNIFICANT USER-VISIBLE CHANGES o Add documentation for RUN.GSEA() function o Remove dependency of RSvgDevice. This package is not available for Windows OS. CHANGES IN VERSION 0.99.1 -------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Add examples in documents NEW FEATURES o Package released