Package cancer. July 10, 2018

Transcription

1 Type Package Package cancer July 10, 2018 Title A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC. Version Date Author Karim Mezhoud. Nuclear Safety & Security Department. Nuclear Science Center of Tunisia. Maintainer Karim Mezhoud <kmezhoud@gmail.com> The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC). License GPL-2 LazyLoad yes Depends R (>= 3.3), tcltk, tcltk2, cgdsr Imports GSEABase, GSEAlm, tkrplot, genetclassifier, RUnit, Formula, rpart, survival, Biobase, phenotest, circlize, plyr, graphics, stats, utils Suggests testthat (>= ), R.rsp VignetteBuilder R.rsp biocviews GUI, GeneExpression, Software RoxygenNote git_url git_branch RELEASE_3_7 git_last_commit dc44485 git_last_commit_date Date/Publication

2 2 R topics documented: R topics documented: about cancer cancerhelp cancer_vignette cbind.na ClinicalData dialoggeneclassifier dialoggetgenelistmsigdb dialogmetoption dialogmut dialogoptioncircos dialogoptiongsealm dialogoptionphenotest dialogplotoption_skincor dialogsamplinggsea dialogselectfiles_gsea dialogspecificmut dialogsummary_gsea displayintable GeneExpMatrix getcases getcasesgenprofs getcircos getclinicaldatamatrix getclinicdata_multiplecases getcor_expcnamet geteset getgctclsexample getgct_clsfiles getgeneexpmatrix getgenelist getgenelistexample getgenelistfrommsigdb getgenesclassifier getgenestree_multiplecases getgenestree_singlecase getgenprofs getgsealm_diseases getgsealm_variables getintable getlistprofdata getmegaprofdata getmetdatamultiplegenes getmsigdb getmsigdbexample getmsigdbfile getmutdata getphenotest getprofilesdatamultiplegenes getprofilesdatasinglegene

3 about 3 getspecificmut getsummarygsea getsurvival gettextwin GSEA GSEA.Analyze.Sets GSEA.ConsPlot GSEA.EnrichmentScore GSEA.EnrichmentScore GSEA.Gct2Frame GSEA.Gct2Frame GSEA.GeneRanking GSEA.HeatMapPlot GSEA.HeatMapPlot GSEA.NormalizeCols GSEA.NormalizeRows GSEA.ReadClsFile GSEA.Res2Frame GSEA.Threshold GSEA.VarFilter GSEA.write.gct Match_GeneList_MSigDB modaldialog myglobalenv OLD.GSEA.EnrichmentScore plotmodel plot_1gene_2genprofs plot_2genes_1genprof rbind.na Run.GSEA setworkspace testcheckedcasegenprof Index 50 about about cancer about cancer about() dialig box with text

4 4 cancerhelp about() cancer main function main function cancer() open the starting windows with cancer studies myglobalenv <- new.env(parent = emptyenv()) cancer() cancerhelp cancer Help cancer Help cancerhelp() html file with tutorial cancerhelp()

5 cancer_vignette 5 cancer_vignette open pdf vignette open pdf vignette cancer_vignette() open pdf vignette cancer_vignette() cbind.na bind non equal colunm bind non equal colunm cbind.na(..., deparse.level = 1) deparse.level 1 a data frame with merged columns col1 <- c("a","b","c","d") col2 <- c("a", "B", "C") col3 <- cbind.na(col1, col2)

6 6 dialoggeneclassifier ClinicalData ClinicalData Example of Clinical Data data("clinicaldata") Format A data frame with 770 observations on the following 4 variables. DFS_MONTHS a numeric vector DFS_STATUS a factor with levels DiseaseFree Recurred/Progressed OS_MONTHS a numeric vector OS_STATUS a factor with levels DECEASED LIVING a dataframe with clinical data Source cbioportal data("clinicaldata") dialoggeneclassifier Dialogue Box for gene classifier setting: sample size and postprob threshold Dialogue Box for gene classifier setting: sample size and postprob threshold dialoggeneclassifier(lchecked_cases,entrywidth = 10,returnValOnCancel = "ID_CANCEL")

7 dialoggetgenelistmsigdb 7 Lchecked_Cases integer with a number of checked cases entrywidth integer default 10 returnvaloncancel "ID_CANCEL" a dataframe with genes classes load(paste(path.package("cancer"),"/data/gbm_tcgaplottwogenprof.rdata", sep="")) getgenesclassifier() dialoggeneclassifier(1,10,returnvaloncancel = "ID_CANCEL") dialoggetgenelistmsigdb Multi-select choice of gene sets from loaded MSigDB Multi-select choice of gene sets from loaded MSigDB dialoggetgenelistmsigdb(msigdb) MSigDB object with MSigDB. A list of genesets a dataframe with genes classes z <- 7 MSigDB <- readlines(paste(.libpaths(),"/cancer/extdata/msigdb/c5.bp.v4.0.symbols.gmt", sep="")) dialoggetgenelistmsigdb(msigdb)

8 8 dialogmut dialogmetoption Dialog Box to set methylation options Dialog Box to set methylation options dialogmetoption(profdata, k) ProfData adataframe with methylation data k threshold of silencing gene 0:1 a dialog box to set methylation option (threshold of silencing gene) getmetdatamultiplegenes() #dialogmetoption(profdata,0.7) dialogmut Dialog bos to set returned Mutation information Dialog bos to set returned Mutation information dialogmut(title, question, entryinit, entrywidth = 40,returnValOnCancel = "ID_CANCEL") title question entryinit title of the table question entryinit entrywidth 40 returnvaloncancel "ID_CANCEL"

9 dialogoptioncircos 9 a check box with mutations variables dialogmut("title", "question", "entryinit", entrywidth = 40, returnvaloncancel = "ID_CANCEL") dialogoptioncircos Checkbox to select dimensions Checkbox to select dimensions dialogoptioncircos() a checkbox with all dimensions load(paste(path.package("cancer"),"/data/circos.rdata", sep="")) dialogoptioncircos() #getcircos(dimension ="All") dialogoptiongsealm Dialogbox to select variables from Clinical data Dialogbox to select variables from Clinical data dialogoptiongsealm(k,clinicaldata) k integer 1 ClinicalData dataframe with clinical variables

10 10 dialogplotoption_skincor permutaion value, p-value, covariables data(clinicaldata) getoptiongsealm() dialogoptionphenotest Checkbox to select variables from clinical data Checkbox to select variables from clinical data dialogoptionphenotest(eset) eset Expression Set vectors: variables to test Survival status, AGE, p-value load(paste(path.package("cancer"),"/data/prad_michphenotest1021.rdata", sep="")) dialogoptionphenotest(myglobalenv$eset) dialogplotoption_skincor Checkbox to select variables for plotting Checkbox to select variables for plotting dialogplotoption_skincor(s)

11 dialogsamplinggsea 11 s integer number of Studies Dialog box with setting of correlation method load(paste(path.package("cancer"),"/data/gbm_tcgaplottwogenprof.rdata", sep="")) dialogplotoption_skincor(1) dialogsamplinggsea Dialog Box for Sampling patients from expression profile data used for GSEA-R (Broad Institute) Dialog Box for Sampling patients from expression profile data used for GSEA-R (Broad Institute) dialogsamplinggsea( Lchecked_Cases,entryWidth = 10,returnValOnCancel = "ID_CANCEL") Lchecked_Cases Number of checked Cases entrywidth 10 returnvaloncancel "ID_CANCEL" A vector with sampling size Run.GSEA() #dialogsamplinggsea(1,entrywidth=10,returnvaloncancel = "ID_CANCEL")

12 12 dialogspecificmut dialogselectfiles_gsea Dialog Box to Select GCT, CLS, GMT and output Files for GSEA-R (Broad Institute) Dialog Box to Select GCT, CLS, GMT and output Files for GSEA-R (Broad Institute) dialogselectfiles_gsea() A vector with files paths dialogselectfiles_gsea() dialogspecificmut dialog box to Specify Mutation using Regular Expression. Search specific mutation using regular expression. dialog box to Specify Mutation using Regular Expression. Search specific mutation using regular expression. getspecificmut() a a dataframe with specific mutation informations getspecificmut()

13 dialogsummary_gsea 13 dialogsummary_gsea Dialog Box to specify phenotype (variable) used in last GSEA-R to get Summary Results. This function ask the user to specify the phenotype (variable). Dialog Box to specify phenotype (variable) used in last GSEA-R to get Summary Results. This function ask the user to specify the phenotype (variable). dialogsummary_gsea(variable,returnvaloncancel ="ID_CANCEL") Variable phenotype returnvaloncancel "ID_CANCEL" variables #Run.GSEA() #getsummarygsea() displayintable Display matrix in tcltk table Display matrix in tcltk table displayintable(tclarray,title="",height=-1,width=-1,nrow=-1,ncol=-1) tclarray a dataframe title title of the table height -1 width -1 nrow -1 ncol -1

14 14 GeneExpMatrix display a Table data(clinicaldata) getintable(table= ClinicalData, title= "Clinical Data") GeneExpMatrix GeneExpMatrix Example of GeneExpMatrix data("geneexpmatrix") Format A data frame with 958 observations on the following 18 variables. BEGAIN a numeric vector CD83 a numeric vector CD93 a numeric vector CEP164 a numeric vector FOXN2 a numeric vector IGFBP2 a numeric vector IL18 a numeric vector KDELR1 a numeric vector NCSTN a numeric vector NOTCH2 a numeric vector NPY a numeric vector NT5E a numeric vector PARP4 a numeric vector SIGLEC1 a numeric vector SLC16A2 a numeric vector SLC35B1 a numeric vector SLC9A2 a numeric vector VPS16 a numeric vector

15 getcases 15 Details Source example of gene expression a dataframe of gene expression cbioportal References cbioportal data(geneexpmatrix) ## maybe str(geneexpmatrix) ; plot(geneexpmatrix)... getcases Get cases for selected Studies. The Cases are the descrption of the samples from patients. The samples can be subdivided by the type of assays as, sequencing, CNA, Mutation, Methylation. Get cases for selected Studies. The Cases are the descrption of the samples from patients. The samples can be subdivided by the type of assays as, sequencing, CNA, Mutation, Methylation. getcases() a dataframe with cases # Create CGDS object cgds<-cgds(" # Get list of cancer studies at server Studies <- getcancerstudies(cgds)[,2] # Get available case lists (collection of samples) for a given cancer study mycancerstudy <- getcancerstudies(cgds)[2,1] mycaselist <- getcaselists(cgds,mycancerstudy)[1,1] ##getcases()

16 16 getcircos getcasesgenprofs get Cases and Genetic Profiles of selected Studies. get Cases and Genetic Profiles of selected Studies. getcasesgenprofs() This function is run by the "Get Cases and Genetic Profiles for selected Studies in starting window. This function needs to select at least one study and display Cases and genetic profiles in the main window. ##Load Session load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) ## load Cases and Genetic Profiles getcasesgenprofs() getcircos get Circos Layout for selected studies and selected dimensions get Circos Layout for selected studies and selected dimensions getcircos(dimension) dimension string (All,mRNA, CNA, Met,RPPA, mirna, Mut) a plot with Circos style load(paste(path.package("cancer"),"/data/circos.rdata", sep="")) getcircos(dimension ="All")

17 getclinicaldatamatrix 17 getclinicaldatamatrix get matrix with clinical from file get matrix with clinical from file getclinicaldatamatrix() dataframe of clinicaldata load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) getclinicaldatamatrix() getclinicdata_multiplecases get Clinical Data for Multiple Cases. User needs to select at least one case to run this function. Get clinical data for more one or multiple cases. get Clinical Data for Multiple Cases. User needs to select at least one case to run this function. Get clinical data for more one or multiple cases. getclinicdata_multiplecases(getsummarygseaexists) getsummarygseaexists if equal to 0, the clinical data is displayed in table. if the argument is equal to 1, the clinical data is used to summarise GSEA analysis results. dataframe with clinical data

18 18 getcor_expcnamet ##Load Session load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) ## Select Case myglobalenv$curselectcases <- 2 ## get Clinical data getclinicdata_multiplecases(getsummarygseaexists = 0) getcor_expcnamet Get gene correlation for multiple dimensions. Get gene correlation for multiple dimensions. getcor_expcnamet(listmatrix, dimension) ListMatrix dimension is a List of numeric matrices Exp,CNA, Met, mirna, RPPA correlation matrix load(paste(path.package("cancer"),"/data/circos.rdata", sep="")) getlistprofdata() getcor_expcnamet(myglobalenv$listprofdata$expression, dimension="mrna") head(myglobalenv$cor_exp)

19 geteset 19 geteset Built Expression Set (eset) from profile data. Built Expression Set (eset) from profile data. geteset() ExpressionSet f <- 9 load(paste(.libpaths(),"cancer/data/prad_michphenotest1021", sep="")) geteset() getgctclsexample get GCT and CLS example files. get GCT and CLS example files. getgctclsexample() GCT and CLS files ## Load workspace getgctclsexample()

20 20 getgeneexpmatrix getgct_clsfiles get Profile (GCT file) and Phenotype (CLS file) Data from Disease. get Profile (GCT file) and Phenotype (CLS file) Data from Disease. getgct_clsfiles() GCT and CLS files paths getgct_clsfiles() getgeneexpmatrix get matrix with gene expression from file get matrix with gene expression from file getgeneexpmatrix() dataframe of gene expression load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) getgeneexpmatrix()

21 getgenelist 21 getgenelist User needs to specify which gene is interesting to get genomic cancer data. The gene must be with Symbol and one gene by line. User needs to specify which gene is interesting to get genomic cancer data. The gene must be with Symbol and one gene by line. getgenelist() Gene list path of file myglobalenv <- new.env(parent = emptyenv()) getgenelist() getgenelistexample get Gene List from examples. User can select one from available gene list get Gene List from examples. User can select one from available gene list getgenelistexample() Gene list path of file myglobalenv <- new.env(parent = emptyenv()) getgenelistexample()

22 22 getgenesclassifier getgenelistfrommsigdb get gene list from MSigDB get gene list from MSigDB getgenelistfrommsigdb() a vector with gene list load(paste(path.package("cancer"),"/data/brca_tcgagsealm1021.rdata", sep="")) getgenelistfrommsigdb() getgenesclassifier get Genes Classifier get Genes Classifier getgenesclassifier() a data frma with genes classes x <- 0 load(paste(.libpaths(),"/cancer/data/brca_tcga73genes.rdata", sep="")) getgenesclassifier()

23 getgenestree_multiplecases 23 getgenestree_multiplecases Get successively trees of genes list for multiple cases Get successively trees of genes list for multiple cases getgenestree_multiplecases(entrywidth = 10) entrywidth 10 plot tree q <- load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) load(paste(.libpaths(),"/cancer/data/brca_tcga73genes.rdata", sep="")) getgenestree_multiplecases(entrywidth = 10) getgenestree_singlecase classify genes in tree for two phenotypes in the same case(disease). classify genes in tree for two phenotypes in the same case(disease). getgenestree_singlecase() tree plot load(paste(path.package("cancer"),"/data/prad_michphenotest1021.rdata", sep="")) getgenestree_singlecase()

24 24 getgsealm_diseases getgenprofs Get Genetic Profile from selected Studies Get Genetic Profile from selected Studies getgenprofs() dataframe with genetic profil cgds<-cgds(" # Get list of cancer studies at server Studies <- getcancerstudies(cgds)[,2] # Get available case lists (collection of samples) for a given cancer study mycancerstudy <- getcancerstudies(cgds)[2,1] mycaselist <- getcaselists(cgds,mycancerstudy)[1,1] # Get available genetic profiles mygeneticprofile <- getgeneticprofiles(cgds,mycancerstudy)[4,1] getgenprofs() getgsealm_diseases get GSEA linear modeling by studies (diseases) get GSEA linear modeling by studies (diseases) getgsealm_diseases() a dataframe with annotation (GO, BP) load(paste(.libpaths(),"/cancer/data/ucec_tcga_pubgsea1021.rdata", sep="")) getgsealm_diseases

25 getgsealm_variables 25 getgsealm_variables get GSEA linear modeling by variables (phenotype) get GSEA linear modeling by variables (phenotype) getgsealm_variables() a dataframe with annotation (GO, BP) x <- 3 load(paste(.libpaths(),"/cancer/data/ucec_tcga_pubgsea1021.rdata", sep="")) getgsealm_variables() getintable get dataframe in TK/TCL table get dataframe in TK/TCL table getintable(table,title) table title Dataframe string a title of the table display a Table data(clinicaldata) getintable(table= ClinicalData, title= "Clinical Data")

26 26 getmegaprofdata getlistprofdata get a list of Profile Data of every available dimensions. This function load matrices of every dimension (Exp, CNA, Met, RPPA,miRNA,Mut) and save them in a list for every disease. get a list of Profile Data of every available dimensions. This function load matrices of every dimension (Exp, CNA, Met, RPPA,miRNA,Mut) and save them in a list for every disease. getlistprofdata() a list of data frame with Profiles Data load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) getlistprofdata() head(myglobalenv$profdata$expression) getmegaprofdata Get profile data for more than 500 genes list. Get profile data for more than 500 genes list. getmegaprofdata(megagenelist,k) MegaGeneList Genelist >500 k integer number of studies dataframewith profile data

27 getmetdatamultiplegenes 27 myglobalenv <- new.env(parent = emptyenv()) load(paste(path.package("cancer"),"/data/brca_tcgagsealm1021.rdata", sep="")) getmegaprofdata(myglobaenv$megagenelist,1) getmetdatamultiplegenes get Methylation data for multiple genes get Methylation data for multiple genes getmetdatamultiplegenes() a a dataframe with mean and median of methylation rate (threshold of silencing gene) getmetdatamultiplegenes() getmsigdb Reduce MSigDB size for only gene list Reduce MSigDB size for only gene list getmsigdb(eset, k) eset k Expression Set integer Number of studies

28 28 getmsigdbfile MSigDB for user gene List d <- 7 setworkspace() getmsigdb(eset = myglobalenv$esetclassifier,k = 1) getmsigdbexample get example of.gmt file from MSigDB (Broad Institute) get example of.gmt file from MSigDB (Broad Institute) getmsigdbexample() path of GMT file load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) getmsigdbexample() getmsigdbfile Dialog Box to Select MSigDB Files from drive Dialog Box to Select MSigDB Files from drive getmsigdbfile() A path of MSigDB file

29 getmutdata 29 f <- 5+2 load(paste(path.package("cancer"),"/data/prad_michphenotest1021", sep="")) geteset() getmsigdbfile() getmutdata get Mutation data for multiple genes get Mutation data for multiple genes getmutdata() a a dataframe with mutation informations getmutdata() getphenotest Associate phenotype to Studies (cancers) Associate phenotype to Studies (cancers) getphenotest() a dataframe with disease/ variables association

30 30 getprofilesdatasinglegene load(paste(path.package("cancer"),"/data/prad_michphenotest1021.rdata", sep="")) getphenotest(myglobalenv$eset) getprofilesdatamultiplegenes get Profles Data of multiple genes get Profles Data of multiple genes getprofilesdatamultiplegenes(getsummarygseaexists) getsummarygseaexists if equal to 0, the clinical data is displayed in table. if the argument is equal to 1, the clinical data is used to summarise GSEA analysis results. a file with a dataframe of profle data load(paste(path.package("cancer"),"/data/prad_michphenotest1021.rdata", sep="")) getprofilesdatamultiplegenes(getsummarygseaexists = 0) getprofilesdatasinglegene get Profiles Data for a Single Gene. get Profiles Data for a Single Gene. getprofilesdatasinglegene()

31 getspecificmut 31 dataframe with profiles data for a single gene load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) ## Select Case from Breast Cancer myglobalenv$curselectcases <- 9 ##Select Genetic Profile from Breast Cancer myglobalenv$curselectgenprofs <- 4 ## get Specific Mutation data for 73 Genes list getprofilesdatasinglegene() getspecificmut get specific Mutation data for multiple genes get specific Mutation data for multiple genes getspecificmut() a a dataframe with specific mutation informations getspecificmut() getsummarygsea get Summary results from GSEA-R (Broad Institute) get Summary results from GSEA-R (Broad Institute) getsummarygsea()

32 32 getsurvival Dataframe with summary results Run.GSEA() getsummarygsea() getsurvival Survival plot Survival plot getsurvival(coxph) Coxph if Coxph = 0 : plot Kaplan-Meier curves else Coxph= 1 : plot Cox Proportional Hazard Model Survival plot surv <- 11 load(paste(.libpaths(),"/cancer/data/gbm_tcgaplottwogenprof.rdata", sep="")) getsurvival(coxph = 1)

33 gettextwin 33 gettextwin get text in tcltk windows get text in tcltk windows gettextwin(text) text string tcltk windows with text text <- "mytext" gettextwin(text) GSEA GSEA-R (Broad Institute) See GSEA Author(s) Subramanian, Tamayo, et al. (2005, PNAS 102, ) and Mootha, Lindgren, et al. (2003, Nat Genet 34, ) library(cancer) ## Load workspace ##Run.GSEA()

34 34 GSEA.Analyze.Sets GSEA.Analyze.Sets GSEA.Analyze.Sets GSEA.Analyze.Sets(directory,topgs="",non.interactive.run= FALSE,height=12,width=17) directory topgs topgs = 20 directory= fname.output non.interactive.run non.interactive.run= FALSE height width height=16 width=16 GSEA.Analyze.Sets Author(s) Subramanian, Tamayo, et al. (2005, PNAS 102, ) and Mootha, Lindgren, et al. (2003, Nat Genet 34, ) References ## Load workspace ##Run.GSEA()

35 GSEA.ConsPlot 35 GSEA.ConsPlot GSEA.ConsPlot GSEA.ConsPlot GSEA.ConsPlot(V, col.names, main = " ", sub = " ", xlab = " ", ylab = " ") V V="Itable" col.names col.names = colnames main main= " " sub sub = " " xlab xlab= " " ylab ylab = " " GSEA.ConsPlot library(cancer) ## Load workspace ##Run.GSEA() GSEA.EnrichmentScore GSEA.EnrichmentScore GSEA.EnrichmentScore GSEA.EnrichmentScore(gene.list, gene.set, weighted.score.type = 1, correl.vector = NULL)

36 36 GSEA.EnrichmentScore2 gene.list gene.set weighted.score.type correl.vector GSEA.EnrichmentScore library(cancer) ## Load workspace ##Run.GSEA() GSEA.EnrichmentScore2 GSEA.EnrichmentScore2 GSEA.EnrichmentScore2 GSEA.EnrichmentScore2(gene.list, gene.set, weighted.score.type = 1, correl.vector = NULL) gene.list gene.set weighted.score.type correl.vector GSEA.EnrichmentScore2 library(cancer) ## Load workspace ##Run.GSEA()

37 GSEA.Gct2Frame 37 GSEA.Gct2Frame GSEA.Gct2Frame GSEA.Gct2Frame GSEA.Gct2Frame(filename = "NULL") filename GSEA.GCT2Frame library(cancer) ## Load workspace ##Run.GSEA() GSEA.Gct2Frame2 GSEA.Gct2Frame2 GSEA.Gct2Frame2 GSEA.Gct2Frame2(filename = "NULL") filename GSEA.GCT2Frame2

38 38 GSEA.GeneRanking library(cancer) ## Load workspace ##Run.GSEA() GSEA.GeneRanking GSEA.GeneRanking GSEA.GeneRanking A class.labels gene.labels nperm permutation.type sigma.correction fraction replace reverse.sign GSEA.GeneRanking library(cancer) ## Load workspace ##Run.GSEA()

39 GSEA.HeatMapPlot 39 GSEA.HeatMapPlot GSEA.HeatMapPlot GSEA.HeatMapPlot GSEA.HeatMapPlot library(cancer) ## Load workspace ##Run.GSEA() GSEA.HeatMapPlot2 GSEA.HeatMapPlot2 GSEA.HeatMapPlot2 GSEA.HeatMapPlot2 library(cancer) ## Load workspace ##Run.GSEA()

40 40 GSEA.NormalizeRows GSEA.NormalizeCols GSEA.NormalizeCols GSEA.NormalizeCols GSEA.NormalizeCols(V) V GSEA.NormalizeCols ## Load workspace ##Run.GSEA() GSEA.NormalizeRows GSEA.NormalizeRows GSEA.NormalizeRows GSEA.NormalizeRows(V) V GSEA.NormalizeRows

41 GSEA.ReadClsFile 41 library(cancer) ## Load workspace ##Run.GSEA() GSEA.ReadClsFile GSEA.ReadClsFile GSEA.ReadClsFile GSEA.ReadClsFile(file = "NULL") file GSEA.ReadClsFile ##Run.GSEA() GSEA.Res2Frame GSEA.Res2Frame GSEA.Res2Frame GSEA.Res2Frame(filename = "NULL") filename

42 42 GSEA.Threshold GSEA.NormalizeCols ##Run.GSEA() GSEA.Threshold GSEA.Threshold GSEA.Threshold GSEA.Threshold(V, thres, ceil) V thres ceil GSEA.Threshold ## Load workspace ##Run.GSEA()

43 GSEA.VarFilter 43 GSEA.VarFilter GSEA.VarFilter GSEA.VarFilter GSEA.VarFilter(V, fold, delta, gene.names = "NULL") V fold delta gene.names GSEA.VarFilter ## Load workspace ##Run.GSEA() GSEA.write.gct GSEA.write.gct GSEA.write.gct GSEA.write.gct(gct, filename) gct filename GSEA.Write.gct

44 44 modaldialog ## Load workspace ##Run.GSEA() Match_GeneList_MSigDB Search MSigDb that overlap gene list Search MSigDb that overlap gene list Match_GeneList_MSigDB GeneList load(paste(path.package("cancer"),"/data/prad_michphenotest1021.rdata", sep="")) Match_GeneList_MSigDB() modaldialog Dialog box to specify Gene Symbol. Dialog box to specify Gene Symbol. modaldialog(title, question, entryinit, entrywidth = 40,returnValOnCancel = "ID_CANCEL") title question entryinit string string entryinit entrywidth 40 returnvaloncancel "ID_CANCEL"

45 myglobalenv 45 dialog box load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) ## Select Case from Breast Cancer myglobalenv$curselectcases <- 9 ##Select Genetic Profile from Breast Cancer myglobalenv$curselectgenprofs <- 4 ## get Specific Mutation data for 73 Genes list getprofilesdatasinglegene() myglobalenv myglobalenv Global environment to store cancer variables. Format The format is: <environment: 0xb3eb240> myglobalenv <- new.env(parent = emptyenv()) OLD.GSEA.EnrichmentScore OLD.GSEA.EnrichmentScore OLD.GSEA.EnrichmentScore gene.list gene.set OLD.GSEA.EnchmentScore

46 46 plot_1gene_2genprofs ##Run.GSEA() plotmodel model plotting with tcltk model plotting with tcltk plotmodel(plotcommand, title= "TITLE",hscale=1, vscale=1 ) plotcommand title hscale vscale plotcommand title of plot horizintal scale vertical scale plot load(paste(path.package("cancer"),"/data/gbm_tcgaplottwogenprof.rdata", sep="")) plot_1gene_2genprofs() plot_1gene_2genprofs Plotting two genetic profiles for one Gene Plotting two genetic profiles for one Gene plot_1gene_2genprofs()

47 plot_2genes_1genprof 47 plot load(paste(path.package("cancer"),"/data/gbm_tcgaplottwogenprof.rdata", sep="")) plot_1gene_2genprofs() plot_2genes_1genprof plot correlation of two genes expressions. plot correlation of two genes expressions. plot_2genes_1genprof() plot plot_2genes_1genprof() rbind.na bind non equal row bind non equal row rbind.na(..., deparse.level = 1) deparse.level 1

48 48 setworkspace a data frame with merged rows row1 <- c("a","b","c","d") row2 <- c("a", "B", "C") row3 <- rbind.na(row1, row2) Run.GSEA The main function to run GSEA-R from Broad Institute The main function to run GSEA-R from Broad Institute Run.GSEA() A vector with sampling size Run.GSEA() setworkspace Setting work Directory and output folders.at starting window, user needs to set work directory for output data. The function is foud in File menu. Setting work Directory and output folders.at starting window, user needs to set work directory for output data. The function is foud in File menu. setworkspace()

49 testcheckedcasegenprof 49 paths of output files load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) setworkspace() testcheckedcasegenprof Testing checked appropriate Cases for appropriate Genetic profiles. Testing checked appropriate Cases for appropriate Genetic profiles. testcheckedcasegenprof() dialog box with warning message load(paste(path.package("cancer"),"/data/brca_tcga73genes.rdata", sep="")) testcheckedcasegenprof()

50 Index Topic datasets ClinicalData, 6 GeneExpMatrix, 14 myglobalenv, 45 about, 3 cancer, 4 cancer_vignette, 5 cancerhelp, 4 cbind.na, 5 ClinicalData, 6 dialoggeneclassifier, 6 dialoggetgenelistmsigdb, 7 dialogmetoption, 8 dialogmut, 8 dialogoptioncircos, 9 dialogoptiongsealm, 9 dialogoptionphenotest, 10 dialogplotoption_skincor, 10 dialogsamplinggsea, 11 dialogselectfiles_gsea, 12 dialogspecificmut, 12 dialogsummary_gsea, 13 displayintable, 13 GeneExpMatrix, 14 getcases, 15 getcasesgenprofs, 16 getcircos, 16 getclinicaldatamatrix, 17 getclinicdata_multiplecases, 17 getcor_expcnamet, 18 geteset, 19 getgct_clsfiles, 20 getgctclsexample, 19 getgeneexpmatrix, 20 getgenelist, 21 getgenelistexample, 21 getgenelistfrommsigdb, 22 getgenesclassifier, 22 getgenestree_multiplecases, 23 getgenestree_singlecase, 23 getgenprofs, 24 getgsealm_diseases, 24 getgsealm_variables, 25 getintable, 25 getlistprofdata, 26 getmegaprofdata, 26 getmetdatamultiplegenes, 27 getmsigdb, 27 getmsigdbexample, 28 getmsigdbfile, 28 getmutdata, 29 getphenotest, 29 getprofilesdatamultiplegenes, 30 getprofilesdatasinglegene, 30 getspecificmut, 31 getsummarygsea, 31 getsurvival, 32 gettextwin, 33 GSEA, 33 GSEA.Analyze.Sets, 34 GSEA.ConsPlot, 35 GSEA.EnrichmentScore, 35 GSEA.EnrichmentScore2, 36 GSEA.Gct2Frame, 37 GSEA.Gct2Frame2, 37 GSEA.GeneRanking, 38 GSEA.HeatMapPlot, 39 GSEA.HeatMapPlot2, 39 GSEA.NormalizeCols, 40 GSEA.NormalizeRows, 40 GSEA.ReadClsFile, 41 GSEA.Res2Frame, 41 GSEA.Threshold, 42 GSEA.VarFilter, 43 GSEA.write.gct, 43 Match_GeneList_MSigDB, 44 modaldialog, 44 myglobalenv, 45 OLD.GSEA.EnrichmentScore, 45 plot_1gene_2genprofs, 46 plot_2genes_1genprof, 47 50

51 INDEX 51 plotmodel, 46 rbind.na, 47 Run.GSEA, 48 setworkspace, 48 testcheckedcasegenprof, 49