Files in mssm-msf-2019/BiostatsALL

R/CalculateCorrMatrix.R R/ComBat_MSF.R R/CorrelationHeatmap_Samples.R R/CreateOutputsMA.R R/CreateOutputsRNASeq.R R/Create_GSEAInput.R R/DoCluster.R R/DoCluster2.R R/DoCorrelationPlotwithStars.R R/DoHeatmap.3_MSF.R R/DoHeatmap.R R/DoHeatmapSamples.R R/Do_pHeatmapSamples.R R/FromEbfit2DEGTable.R R/FromEbfit2DEGTable_GSVA.R R/FromEbfit2Table.R R/FromEbfit2Table_GSVA.R R/HyperGeneSetCollection_MSF.R R/HyperGeneSetCollection_MSF_windows.r R/LazyTableOne.R R/List2mat.R R/NormalizeByPatient.R R/PSMatchit.R R/PlateDesignFunction.R R/Resume.R R/Run.swindel.sims.R R/RunCombat.R R/RunCombatMat.R R/RunCombat_MSF.R R/RunGeneSetCollection_MSF.R R/RunLogitXwith3levels.R R/add.dimnames2db.R R/add.names2vector.R R/analyzeGeneSetCollections_MSF.R R/analyzeGeneSetCollections_MSF_windows.r R/annoXMouseHuman.R R/annoXeset.R R/auxBiplot.R R/calc.BMI.R R/calcFCH.R R/cluster_mat.R R/colChoice.2.R R/collapseduplicatesids.R R/collapsefcn.R R/convert_annotations.R R/cor.prob.pearson.R R/cor.prob.spearman.R R/count.n.R R/cr_eqn.R R/createNiceRow.R R/createNiceTable.R R/createTable_MeanSDTtest_AllContinuous.R R/deletePathway.R R/dis.cors.R R/doBarPlot.R R/doBoxplot.R R/doClusterTableFCH_fromMatrix.R R/doSwindellPlot.R R/doVenn.R R/dogetPathByCoef.R R/dowordcloud.R R/draw_annotation_legend.R R/draw_annotation_names.R R/draw_annotations.R R/draw_colnames.R R/draw_connection.R R/draw_dendrogram.R R/draw_legend.R R/draw_main.R R/draw_matrix.R R/draw_rownames.R R/ellipsoid.Fox.R R/find_coordinates.R R/find_gaps.R R/firstelementfcn.R R/form1list2D.R R/from2list2D.R R/fromPtoCol.R R/generate_annotation_colours.R R/generate_breaks.R R/getAllDEGs.R R/getAnnotationTable.R R/getBatchDateFromEset.R R/getBestModel.R R/getMeGoSeqfrom_BigTab.R R/getMeGoSeqfrom_BigTab_Meds.R R/getMeanCI.by.Path.R R/getModels_Caret.R R/getModels_Caret_JCR.R R/getMultipleMeanandCI.by.Path.R R/getMultipleZscore.by.Path.R R/getPCAs.R R/getSymbolByX.R R/getZs.R R/getZscore.R R/getZscore.by.Path.R R/get_naBaseOCF.R R/get_naBestOCF.R R/get_naLOCF.R R/get_naSPLINE.R R/get_naWorstOCF.R R/getgray.R R/getlimmaCIs.R R/getstar.R R/ggDendogram_MSF.R R/givecolnames.R R/gsvaAladin.R R/hack_mclapply.r R/heatmap.3.R R/heatmap_motor.R R/identity2.R R/is.na2.R R/kmeans_pheatmap.R R/limma.getMeansCI.R R/lm_eqn.R R/lo.R R/makeGSEApheno.R R/makenames_MSF.R R/mapvalues_toNA.R R/mclapply.windows.r R/mgsub.R R/multiplot.R R/myfancy_findLargest.R R/mylog10.R R/mylog2.R R/nmissing.R R/normDataWithin.R R/pInt.R R/pheatmap_msf.R R/plot.pvca.R R/plotROCbyGroups.R R/prepareGSEArnk.R R/prepareGSEArnkRNASeq.R R/prettyp.R R/printAOVPVal.R R/printChiSqPVal.R R/printFisherPVal.R R/printKruskalPVal.R R/printLogicalPct.R R/printMeanMinMax.R R/printMeanSD.R R/printMeanSDn.R R/printMedianQ13.R R/printPVal.R R/printTtestPoolPVal.R R/printTtestSattPVal.R R/printWilcoxPVal.R R/processGMT.R R/pvcaBatchAssess.MSF.R R/readGmt.R R/readGmt2.R R/renamecols.R R/savecorrplot.R R/savexlsx.R R/scale2breaks.R R/scale_colours.R R/scale_mat.R R/scale_rows.R R/scale_vec_colours.R R/scatter3d.Fox.R R/sciNotation.R R/spearman_eqn.R R/stackchar.R R/stat_ellipse.R R/stat_ellipse_byFox.R R/summarySE.R R/summarySEwithin.R R/swindel.sims.R R/treatduplicatesids.R R/uniquenona.R R/vplayout.R man/CalculateCorrMatrix.Rd man/ComBat_MSF.Rd man/CorrelationHeatmap_Samples.Rd man/CreateOutputsMA.Rd man/Create_GSEAInput.Rd man/DoCluster.Rd man/DoCluster2.Rd man/DoCorrelationPlotwithStarts.Rd man/DoHeatmap.3_MSF.Rd man/DoHeatmap.Rd man/DoHeatmapSamples.Rd man/FromEbfit2DEGTable.Rd man/FromEbfit2Table.Rd man/Resume.Rd man/Run.swindel.sims.Rd man/RunCombat.Rd man/RunCombatMat.Rd man/RunCombat_MSF.Rd man/RunGeneSetCollection_MSF.Rd man/annoXMouseHuman.Rd man/annoXeset.Rd man/auxBiplot.Rd man/calcFCH.Rd man/colChoice.2.Rd man/collapseduplicatesids.Rd man/collapsefcn.Rd man/cor.prob.pearson.Rd man/cor.prob.spearman.Rd man/deletePathway.Rd man/dis.cors.Rd man/doBarPlot.Rd man/doClusterTableFCH_fromMatrix.Rd man/doSwindellPlot.Rd man/doVenn.Rd man/dowordcloud.Rd man/ellipsoid.Fox.Rd man/firstelementfcn.Rd man/from1list2D.Rd man/from2list2D.Rd man/fromPtoCol.Rd man/getAllDEGs.Rd man/getAnnotationTable.Rd man/getMeanCI.by.Path.Rd man/getModels_Caret.Rd man/getMultipleMeanCI.by.Path.Rd man/getMultipleZscore.by.Path.Rd man/getPCAs.Rd man/getSymbolByX.Rd man/getZs.Rd man/getZscore.by.Path.Rd man/getgray.Rd man/getstar.Rd man/ggDendrogram_MSF.Rd man/givecolnames.Rd man/heatmap.3.Rd man/makeGSEApheno.Rd man/makenames_MSF.Rd man/mgsub.Rd man/multiplot.Rd man/mylog10.Rd man/mylog2.Rd man/nmissing.Rd man/normDataWithin.Rd man/prepareGSEArnk.Rd man/prettyp.Rd man/processGMT.Rd man/readGmt.Rd man/readGmt2.Rd man/renamecols.Rd man/scatter3d.Fox.Rd man/sciNotation.Rd man/stackchar.Rd man/summarySE.Rd man/summarySEwithin.Rd man/swindel.sims.Rd man/uniquenona.Rd