Browse code

compress RData files to RDS

kmezhoud authored on 08/05/2019 16:04:01
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 #' @export
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 #'
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 #' @examples
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-#' data(ClinicalData)
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+#' #data(ClinicalData)
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 #' \dontrun{
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 #' getInTable(Table= ClinicalData, title= "Clinical Data")
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 #' }
Browse code

update canceR

Merge branch 'master' into devel

* master: (38 commits)
testing vignette
add .travis.yml file
add image README
rm .travis
Delete .travis.yml
rewrite Doc, test
canceR_vignette
update doc
travis
travis
readme
update
email
email
Circos Doc
NULL
Circos
Survival plot
Survival plot
survival plot
...

# Conflicts:
# .gitignore
# DESCRIPTION
# NAMESPACE
# NEWS
# R/GSEA.1.0.R
# R/Match_GeneList_MSigDB.R
# R/Run.GSEA.1.0.R
# R/about.R
# R/canceR.R
# R/canceRHelp.R
# R/cbind.na.R
# R/dialogGeneClassifier.R
# R/dialogMetOption.R
# R/dialogMut.R
# R/dialogOptionCircos.R
# R/dialogOptionGSEAlm.R
# R/dialogOptionPhenoTest.R
# R/dialogPlotOption_SkinCor.R
# R/dialogSamplingGSEA.R
# R/dialogSelectFiles_GSEA.R
# R/dialogSpecificMut.R
# R/dialogSummary_GSEA.R
# R/dialoggetGeneListMSigDB.R
# R/displayInTable.R
# R/getCases.R
# R/getCasesGenProfs.R
# R/getCircos.R
# R/getClinicData_MultipleCases.R
# R/getClinicalDataMatrix.R
# R/getCor_ExpCNAMet.R
# R/getGCTCLSExample.R
# R/getGCT_CLSfiles.R
# R/getGSEAlm_Diseases.R
# R/getGSEAlm_Variables.R
# R/getGenProfs.R
# R/getGeneExpMatrix.R
# R/getGeneList.R
# R/getGeneListExample.R
# R/getGeneListFromMSigDB.R
# R/getGenesClassifier.R
# R/getGenesTree_MultipleCases.R
# R/getGenesTree_SingleCase.R
# R/getInTable.R
# R/getListProfData.R
# R/getMSigDB.R
# R/getMSigDBExample.R
# R/getMSigDBfile.R
# R/getMegaProfData.R
# R/getMetDataMultipleGenes.R
# R/getMutData.R
# R/getPhenoTest.R
# R/getProfilesDataMultipleGenes.R
# R/getProfilesDataSingleGene.R
# R/getSpecificMut.R
# R/getSummaryGSEA.R
# R/getSurvival.R
# R/getTextWin.R
# R/geteSet.R
# R/modalDialog.R
# R/plotModel.R
# R/plot_1Gene_2GenProfs.R
# R/plot_2Genes_1GenProf.R
# R/rbind.na.R
# R/setWorkspace.R
# R/testCheckedCaseGenProf.R
# canceR.Rproj
# data/Circos.RData
# data/ClinicalData.txt
# data/GSEA.1.0.R
# data/GeneExpMatrix.txt
# data/brca_tcga73genes.RData
# data/brca_tcgaClassifier223.RData
# data/brca_tcgaGSEAlm1021.RData
# data/gbm_tcgaPlotTwoGenProf.RData
# data/prad_michPhenoTest1021.RData
# data/ucec_tcga_pubGSEA1021.RData
# inst/canceR.html
# inst/canceR_ind.html
# inst/canceRs.html
# inst/extdata/GeneList/102.txt
# inst/extdata/GeneList/1021.txt
# inst/extdata/GeneList/223.txt
# inst/extdata/GeneList/73.txt
# inst/extdata/GeneList/DNA_damage_Response.txt
# inst/extdata/GeneList/Glioblastoma_RTK_Ras_PI3K_AKT_Signaling.txt
# inst/extdata/GeneList/INvasion_and_Metastasis.txt
# inst/extdata/GeneList/ProstateCancer_AR_and_Steroid_synthesis_enzymes.txt
# inst/extdata/GeneList/ProstateCancer_DownRegulated_by_Androgen.txt
# inst/extdata/MSigDB/c2.cp.reactome.v4.0.symbols.gmt
# inst/extdata/MSigDB/c5.bp.v4.0.symbols.gmt
# inst/extdata/gct_cls/Lung_Bost_collapsed_symbols_common_Mich_Bost.gct
# inst/extdata/gct_cls/Lung_Boston.cls
# man/ClinicalData.Rd
# man/GSEA.Analyze.Sets.Rd
# man/GSEA.ConsPlot.Rd
# man/GSEA.EnrichmentScore.Rd
# man/GSEA.EnrichmentScore2.Rd
# man/GSEA.Gct2Frame.Rd
# man/GSEA.Gct2Frame2.Rd
# man/GSEA.GeneRanking.Rd
# man/GSEA.HeatMapPlot.Rd
# man/GSEA.HeatMapPlot2.Rd
# man/GSEA.NormalizeCols.Rd
# man/GSEA.NormalizeRows.Rd
# man/GSEA.Rd
# man/GSEA.ReadClsFile.Rd
# man/GSEA.Res2Frame.Rd
# man/GSEA.Threshold.Rd
# man/GSEA.VarFilter.Rd
# man/GSEA.write.gct.Rd
# man/GeneExpMatrix.Rd
# man/Match_GeneList_MSigDB.Rd
# man/OLD.GSEA.EnrichmentScore.Rd
# man/Run.GSEA.Rd
# man/about.Rd
# man/canceR.Rd
# man/canceRHelp.Rd
# man/canceR_Vignette.Rd
# man/cbind.na.Rd
# man/dialogGeneClassifier.Rd
# man/dialogMetOption.Rd
# man/dialogMut.Rd
# man/dialogOptionCircos.Rd
# man/dialogOptionGSEAlm.Rd
# man/dialogOptionPhenoTest.Rd
# man/dialogPlotOption_SkinCor.Rd
# man/dialogSamplingGSEA.Rd
# man/dialogSelectFiles_GSEA.Rd
# man/dialogSpecificMut.Rd
# man/dialogSummary_GSEA.Rd
# man/dialoggetGeneListMSigDB.Rd
# man/displayInTable.Rd
# man/getCases.Rd
# man/getCasesGenProfs.Rd
# man/getCircos.Rd
# man/getClinicData_MultipleCases.Rd
# man/getClinicalDataMatrix.Rd
# man/getCor_ExpCNAMet.Rd
# man/getGCTCLSExample.Rd
# man/getGCT_CLSfiles.Rd
# man/getGSEAlm_Diseases.Rd
# man/getGSEAlm_Variables.Rd
# man/getGenProfs.Rd
# man/getGeneExpMatrix.Rd
# man/getGeneList.Rd
# man/getGeneListExample.Rd
# man/getGeneListFromMSigDB.Rd
# man/getGenesClassifier.Rd
# man/getGenesTree_MultipleCases.Rd
# man/getGenesTree_SingleCase.Rd
# man/getInTable.Rd
# man/getListProfData.Rd
# man/getMSigDB.Rd
# man/getMSigDBExample.Rd
# man/getMSigDBfile.Rd
# man/getMegaProfData.Rd
# man/getMetDataMultipleGenes.Rd
# man/getMutData.Rd
# man/getPhenoTest.Rd
# man/getProfilesDataMultipleGenes.Rd
# man/getProfilesDataSingleGene.Rd
# man/getSpecificMut.Rd
# man/getSummaryGSEA.Rd
# man/getSurvival.Rd
# man/getTextWin.Rd
# man/geteSet.Rd
# man/modalDialog.Rd
# man/myGlobalEnv.Rd
# man/plotModel.Rd
# man/plot_1Gene_2GenProfs.Rd
# man/plot_2Genes_1GenProf.Rd
# man/rbind.na.Rd
# man/setWorkspace.Rd
# man/testCheckedCaseGenProf.Rd
# vignettes/.gitignore
# vignettes/canceR.bib
# vignettes/canceR.pdf

From: Karim Mezhoud <Mezhoud@MBP-de-MacBook.lan>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR@115378 bc3139a8-67e5-0310-9ffc-ced21a209358

Karim Mezhoud authored on 29/03/2016 20:42:23
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old mode 100644
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new mode 100755
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+#' get dataframe in TK/TCL table
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+#' @usage
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+#' getInTable(table,title)
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+#' @param table Dataframe
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+#' @param title string a title of the table
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+#' @return display a Table
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+#' @export
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+#'
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+#' @examples
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+#' data(ClinicalData)
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+#' \dontrun{
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+#' getInTable(Table= ClinicalData, title= "Clinical Data")
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+#' }
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+
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 getInTable <- function(table,title){
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 matrix <-rbind(colnames(table), table)
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 matrix1 <- cbind(row.names(matrix), matrix)
Browse code

add package muscle and canceR

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR@100351 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 07/03/2015 00:46:17
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+getInTable <- function(table,title){
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+matrix <-rbind(colnames(table), table)
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+matrix1 <- cbind(row.names(matrix), matrix)
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+matrix1 <- t(t(matrix1))
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+
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+# Define a Tcl array and initialize it to that matrix :
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+tclArray1 <- tclArray()
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+for (i in (1:length(matrix1[,1]))){
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+    for (j in (1:length(matrix1[1,]))){
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+        tclArray1[[i-1,j-1]] <- matrix1[i,j]
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+    }
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+}
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+#Table_Title<- paste("SD:",StudyRefCase[k],"_","GenProf:",curselectGenProfs_forStudy[k],"_","CASE:",curselectCases_forStudy[k],".gct")
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+table1 <- displayInTable(tclArray1,title= title ,nrow=nrow(matrix1),ncol=ncol(matrix1),height=30,width=20)
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+
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+}
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\ No newline at end of file