| Title: | A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC |
|---|---|
| Description: | 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). |
| Authors: | Karim Mezhoud. Nuclear Safety & Security Department. Nuclear Science Center of Tunisia. |
| Maintainer: | Karim Mezhoud <[email protected]> |
| License: | GPL-2 |
| Version: | 1.39.0 |
| Built: | 2024-06-30 06:02:23 UTC |
| Source: | https://github.com/bioc/canceR |
about canceR
about()about()
dialig box with text
## Not run: about() ## End(Not run)## Not run: about() ## End(Not run)
main function
canceR()canceR()
open the starting windows with cancer studies
ENV <- new.env(parent = emptyenv()) ## Not run: canceR() ## End(Not run)ENV <- new.env(parent = emptyenv()) ## Not run: canceR() ## End(Not run)
canceR Report Issue
canceR_Issue()canceR_Issue()
link to github issues
## Not run: canceR_Issue() ## End(Not run)## Not run: canceR_Issue() ## End(Not run)
open pdf vignette
canceR_Vignette()canceR_Vignette()
open pdf vignette
## Not run: canceR_Vignette() ## End(Not run)## Not run: canceR_Vignette() ## End(Not run)
bind non equal colunm
cbind.na(..., deparse.level = 1)cbind.na(..., deparse.level = 1)
... |
(generalized) vectors or matrices. |
deparse.level |
integer controlling the construction of labels in the case of non-matrix-like arguments (for the default method): deparse.level = 0 constructs no labels; the default, deparse.level = 1 or 2 constructs labels from the argument names. |
a data frame with merged columns
## Not run: col1 <- c("a","b","c","d") col2 <- c("A", "B", "C") col3 <- cbind.na(col1, col2) ## End(Not run)## Not run: col1 <- c("a","b","c","d") col2 <- c("A", "B", "C") col3 <- cbind.na(col1, col2) ## End(Not run)
Creates a CGDS connection object from a CGDS endpoint URL. This object must be passed on to the methods which query the server.
CGDS(url,verbose=FALSE,ploterrormsg='',token=NULL)CGDS(url,verbose=FALSE,ploterrormsg='',token=NULL)
url |
A CGDS URL (required). |
verbose |
A boolean variable specifying verbose output (default FALSE) |
ploterrormsg |
An optional message to display in plots if an error occurs (default ”) |
token |
An optional 'Authorization: Bearer' token to connect to cBioPortal instances that require authentication (default NULL) |
Dialogue Box for gene classifier setting: sample size and postprob threshold
dialogGeneClassifier(Lchecked_Cases,entryWidth = 10,returnValOnCancel = "ID_CANCEL")dialogGeneClassifier(Lchecked_Cases,entryWidth = 10,returnValOnCancel = "ID_CANCEL")
Lchecked_Cases |
integer with a number of checked cases |
entryWidth |
integer default 10 |
returnValOnCancel |
"ID_CANCEL" |
a dataframe with genes classes
readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) ## Not run: getGenesClassifier() dialogGeneClassifier(1,10,returnValOnCancel = "ID_CANCEL") ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) ## Not run: getGenesClassifier() dialogGeneClassifier(1,10,returnValOnCancel = "ID_CANCEL") ## End(Not run)
Multi-select choice of gene sets from loaded MSigDB
dialoggetGeneListMSigDB(MSigDB)dialoggetGeneListMSigDB(MSigDB)
MSigDB |
object with MSigDB. A list of genesets |
a dataframe with genes classes
z <- 7 ## Not run: ##MSigDB <- readLines(paste(.libPaths(),"/canceR/extdata/MSigDB/c5.bp.v4.0.symbols.gmt", sep="")) dialoggetGeneListMSigDB(MSigDB) ## End(Not run)z <- 7 ## Not run: ##MSigDB <- readLines(paste(.libPaths(),"/canceR/extdata/MSigDB/c5.bp.v4.0.symbols.gmt", sep="")) dialoggetGeneListMSigDB(MSigDB) ## End(Not run)
Dialog Box to set methylation options
dialogMetOption(ProfData, k)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)
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getMetDataMultipleGenes() #dialogMetOption(ProfData,0.7) ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getMetDataMultipleGenes() #dialogMetOption(ProfData,0.7) ## End(Not run)
Dialog bos to set returned Mutation information
dialogMut(title, question, entryInit, entryWidth = 40,returnValOnCancel = "ID_CANCEL")dialogMut(title, question, entryInit, entryWidth = 40,returnValOnCancel = "ID_CANCEL")
title |
title of the table |
question |
question |
entryInit |
entryInit |
entryWidth |
40 |
returnValOnCancel |
"ID_CANCEL" |
a check box with mutations variables
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: dialogMut("title", "question", "entryInit", entryWidth = 40, returnValOnCancel = "ID_CANCEL") ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: dialogMut("title", "question", "entryInit", entryWidth = 40, returnValOnCancel = "ID_CANCEL") ## End(Not run)
Checkbox to select dimensions
dialogOptionCircos()dialogOptionCircos()
a checkbox with all dimensions
readRDS(paste(path.package("canceR"),"/extdata/rdata/Circos.rds", sep="")) ## Not run: dialogOptionCircos() #getCircos(dimension ="All") ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/Circos.rds", sep="")) ## Not run: dialogOptionCircos() #getCircos(dimension ="All") ## End(Not run)
Dialogbox to select variables from Clinical data
dialogOptionGSEAlm(k,ClinicalData)dialogOptionGSEAlm(k,ClinicalData)
k |
integer 1 |
ClinicalData |
dataframe with clinical variables |
permutaion value, p-value, coVariables
#data(ClinicalData) ## Not run: getOptionGSEAlm() ## End(Not run)#data(ClinicalData) ## Not run: getOptionGSEAlm() ## End(Not run)
Checkbox to select variables from clinical data
dialogOptionPhenoTest(eSet)dialogOptionPhenoTest(eSet)
eSet |
Expression Set |
vectors: variables to test Survival status, AGE, p-value
readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: dialogOptionPhenoTest(ENV$eSet) ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: dialogOptionPhenoTest(ENV$eSet) ## End(Not run)
Checkbox to select variables for plotting
dialogPlotOption_SkinCor(s)dialogPlotOption_SkinCor(s)
s |
integer number of Studies |
Dialog box with setting of correlation method
readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) ## Not run: dialogPlotOption_SkinCor(1) ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) ## Not run: dialogPlotOption_SkinCor(1) ## End(Not run)
Dialog Box for Sampling patients from expression profile data used for GSEA-R (Broad Institute)
dialogSamplingGSEA(n_checked_GenProf, entryWidth = 10,returnValOnCancel = "ID_CANCEL")dialogSamplingGSEA(n_checked_GenProf, entryWidth = 10,returnValOnCancel = "ID_CANCEL")
n_checked_GenProf |
Number of checked genetic profiles |
entryWidth |
10 |
returnValOnCancel |
"ID_CANCEL" |
A vector with sampling size
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: Run.GSEA() #dialogSamplingGSEA(1,entryWidth=10,returnValOnCancel = "ID_CANCEL") ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: Run.GSEA() #dialogSamplingGSEA(1,entryWidth=10,returnValOnCancel = "ID_CANCEL") ## End(Not run)
Dialog Box to Select GCT, CLS, GMT and output Files for GSEA-R (Broad Institute)
dialogSelectFiles_GSEA()dialogSelectFiles_GSEA()
A vector with files paths
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: dialogSelectFiles_GSEA() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: dialogSelectFiles_GSEA() ## End(Not run)
dialog box to Specify Mutation using Regular Expression. Search specific mutation using regular expression.
getSpecificMut()getSpecificMut()
a a dataframe with specific mutation informations
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getSpecificMut() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getSpecificMut() ## End(Not run)
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")dialogSummary_GSEA(Variable,returnValOnCancel ="ID_CANCEL")
Variable |
phenotype |
returnValOnCancel |
"ID_CANCEL" |
variables
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: #Run.GSEA() #getSummaryGSEA() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: #Run.GSEA() #getSummaryGSEA() ## End(Not run)
Display matrix in tcltk table
displayInTable(tclarray,title="",height=-1,width=-1,nrow=-1,ncol=-1)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 |
display a Table
#data(ClinicalData) ## Not run: getInTable(Table= ClinicalData, title= "Clinical Data") ## End(Not run)#data(ClinicalData) ## Not run: getInTable(Table= ClinicalData, title= "Clinical Data") ## End(Not run)
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()getCases()
a dataframe with cases
cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)
get Cases and Genetic Profiles of selected Studies.
getCasesGenProfs()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.
cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)
get Circos Layout for selected studies and selected dimensions
getCircos(dimension)getCircos(dimension)
dimension |
string (All,mRNA, CNA, Met,RPPA, miRNA, Mut) |
a plot with Circos style
readRDS(paste(path.package("canceR"),"/extdata/rdata/Circos.rds", sep="")) ## Not run: getCircos(dimension ="All") ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/Circos.rds", sep="")) ## Not run: getCircos(dimension ="All") ## End(Not run)
get matrix with clinical from file
getClinicalDataMatrix()getClinicalDataMatrix()
dataframe of clinicaldata
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: getClinicalDataMatrix() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: getClinicalDataMatrix() ## End(Not run)
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)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
##Load Session readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Select Case ENV <- new.env(parent = emptyenv()) ENV$curselectCases <- 2 ## get Clinical data ## Not run: getClinicData_MultipleCases(getSummaryGSEAExists = 0) ## End(Not run)##Load Session readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Select Case ENV <- new.env(parent = emptyenv()) ENV$curselectCases <- 2 ## get Clinical data ## Not run: getClinicData_MultipleCases(getSummaryGSEAExists = 0) ## End(Not run)
Get gene correlation for multiple dimensions.
getCor_ExpCNAMet(ListMatrix, dimension)getCor_ExpCNAMet(ListMatrix, dimension)
ListMatrix |
is a List of numeric matrices |
dimension |
Exp,CNA, Met , miRNA , RPPA |
correlation matrix
readRDS(paste(path.package("canceR"),"/extdata/rdata/Circos.rds", sep="")) ## Not run: getListProfData() getCor_ExpCNAMet(ENV$ListProfData$Expression, dimension="mRNA") head(ENV$Cor_Exp) ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/Circos.rds", sep="")) ## Not run: getListProfData() getCor_ExpCNAMet(ENV$ListProfData$Expression, dimension="mRNA") head(ENV$Cor_Exp) ## End(Not run)
Built Expression Set (eSet) from profile data.
geteSet()geteSet()
ExpressionSet
f <- 9 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) geteSet() ## End(Not run)f <- 9 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) geteSet() ## End(Not run)
get mutation frequency
getFreqMutData(list, GeneList)getFreqMutData(list, GeneList)
list |
a list of data frame with mutation data. Each data frame is for one study |
GeneList |
file name of GeneList examples: "73" |
a data frame with mutation frequency. gene is in rows and study is in column
cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)
get Profile (GCT file) and Phenotype (CLS file) Data from Disease.
getGCT_CLSfiles()getGCT_CLSfiles()
GCT and CLS files paths
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getGCT_CLSfiles() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getGCT_CLSfiles() ## End(Not run)
get GCT and CLS example files.
getGCTCLSExample()getGCTCLSExample()
GCT and CLS files
## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getGCTCLSExample() ## End(Not run)## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getGCTCLSExample() ## End(Not run)
get matrix with gene expression from file
getGeneExpMatrix()getGeneExpMatrix()
dataframe of gene expression
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: getGeneExpMatrix() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: getGeneExpMatrix() ## End(Not run)
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()getGeneList()
Gene list path of file
ENV <- new.env(parent = emptyenv()) ## Not run: getGeneList() ## End(Not run)ENV <- new.env(parent = emptyenv()) ## Not run: getGeneList() ## End(Not run)
get Gene List from examples. User can select one from available gene list
getGeneListExample()getGeneListExample()
Gene list path of file
ENV <- new.env(parent = emptyenv()) ## Not run: getGeneListExample() ## End(Not run)ENV <- new.env(parent = emptyenv()) ## Not run: getGeneListExample() ## End(Not run)
get gene list from MSigDB
getGeneListFromMSigDB()getGeneListFromMSigDB()
a vector with gene list
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcgaGSEAlm1021.rds", sep="")) ## Not run: getGeneListFromMSigDB() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcgaGSEAlm1021.rds", sep="")) ## Not run: getGeneListFromMSigDB() ## End(Not run)
get Genes Classifier
getGenesClassifier()getGenesClassifier()
a data frma with genes classes
x <- 0 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) getGenesClassifier() ## End(Not run)x <- 0 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) getGenesClassifier() ## End(Not run)
Get successively trees of genes list for multiple cases
getGenesTree_MultipleCases(entryWidth = 10)getGenesTree_MultipleCases(entryWidth = 10)
entryWidth |
10 |
plot tree
q <- readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: readRDS(paste(.libPaths(),"/canceR/data/brca_tcga73genes.rds", sep="")) getGenesTree_MultipleCases(entryWidth = 10) ## End(Not run)q <- readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: readRDS(paste(.libPaths(),"/canceR/data/brca_tcga73genes.rds", sep="")) getGenesTree_MultipleCases(entryWidth = 10) ## End(Not run)
classify genes in tree for two phenotypes in the same case(disease).
getGenesTree_SingleCase()getGenesTree_SingleCase()
tree plot
readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: getGenesTree_SingleCase() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: getGenesTree_SingleCase() ## End(Not run)
Get Genetic Profile from selected Studies
getGenProfs()getGenProfs()
dataframe with genetic profil
cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)
get GSEA linear modeling by studies (diseases)
getGSEAlm_Diseases()getGSEAlm_Diseases()
a dataframe with annotation (GO, BP)
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getGSEAlm_Diseases ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getGSEAlm_Diseases ## End(Not run)
get GSEA linear modeling by variables (phenotype)
getGSEAlm_Variables()getGSEAlm_Variables()
a dataframe with annotation (GO, BP)
x <- 3 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) getGSEAlm_Variables() ## End(Not run)x <- 3 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) getGSEAlm_Variables() ## End(Not run)
get dataframe in TK/TCL table
getInTable(table,title)getInTable(table,title)
table |
Dataframe |
title |
string a title of the table |
display a Table
#data(ClinicalData) ## Not run: getInTable(Table= ClinicalData, title= "Clinical Data") ## End(Not run)#data(ClinicalData) ## Not run: getInTable(Table= ClinicalData, title= "Clinical Data") ## End(Not run)
Get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...)
getListProfData(checked_Studies, geneList)getListProfData(checked_Studies, geneList)
checked_Studies |
checked studies in corresponding panel (input$StudiesIDCircos, input$StudiesIDReactome). |
geneList |
GeneList with Hugo Symbol |
A LIST of profiles data (CNA, mRNA, Methylation, Mutation, miRNA, RPPA). Each dimension content a list of studies.
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: getListProfData() head(ENV$ProfData$Expression) ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: getListProfData() head(ENV$ProfData$Expression) ## End(Not run)
Get profile data for more than 500 genes list.
getMegaProfData(MegaGeneList,k)getMegaProfData(MegaGeneList,k)
MegaGeneList |
Genelist >500 |
k |
integer number of studies |
dataframewith profile data
myGlobalEnv <- new.env(parent = emptyenv()) readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcgaGSEAlm1021.rds", sep="")) ## Not run: getMegaProfData(myGlobaEnv$MegaGeneList,1) ## End(Not run)myGlobalEnv <- new.env(parent = emptyenv()) readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcgaGSEAlm1021.rds", sep="")) ## Not run: getMegaProfData(myGlobaEnv$MegaGeneList,1) ## End(Not run)
get Methylation data for multiple genes
getMetDataMultipleGenes()getMetDataMultipleGenes()
a a dataframe with mean and median of methylation rate (threshold of silencing gene)
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getMetDataMultipleGenes() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getMetDataMultipleGenes() ## End(Not run)
Reduce MSigDB size for only gene list
getMSigDB(eSet, k)getMSigDB(eSet, k)
eSet |
Expression Set |
k |
integer Number of studies |
MSigDB for user gene List
d <- 7 ## Not run: setWorkspace() getMSigDB(eSet = ENV$eSetClassifier,k = 1) ## End(Not run)d <- 7 ## Not run: setWorkspace() getMSigDB(eSet = ENV$eSetClassifier,k = 1) ## End(Not run)
get example of .gmt file from MSigDB (Broad Institute)
getMSigDBExample()getMSigDBExample()
path of GMT file
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: getMSigDBExample() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: getMSigDBExample() ## End(Not run)
Dialog Box to Select MSigDB Files from drive
getMSigDBfile()getMSigDBfile()
A path of MSigDB file
f <- 5+2 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) geteSet() getMSigDBfile() ## End(Not run)f <- 5+2 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) geteSet() getMSigDBfile() ## End(Not run)
get Mutation data for multiple genes
getMutData()getMutData()
a a dataframe with mutation informations
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getMutData() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getMutData() ## End(Not run)
Associate phenotype to Studies (cancers)
getPhenoTest()getPhenoTest()
a dataframe with disease/ variables association
readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: getPhenoTest(ENV$eSet) ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: getPhenoTest(ENV$eSet) ## End(Not run)
Search and get genetic profiles (CNA,mRNA, Methylation, Mutation...)
getProfData(study,genProf, listGenProf, GeneList, Mut)getProfData(study,genProf, listGenProf, GeneList, Mut)
study |
Study ID |
genProf |
Genetic Profile id (cancer_study_id_[mutations, cna, methylation, mrna ]). |
listGenProf |
A list of Genetic Profiles for one study. |
GeneList |
A list of genes |
Mut |
Condition to set if the genetic profile is mutation or not (0,1) |
See https://github.com/kmezhoud/bioCancer/wiki
A data frame with Genetic profile
cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)
get Profles Data of multiple genes
getProfilesDataMultipleGenes(getSummaryGSEAExists)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
readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: getProfilesDataMultipleGenes(getSummaryGSEAExists = 0) ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: getProfilesDataMultipleGenes(getSummaryGSEAExists = 0) ## End(Not run)
get Profiles Data for a Single Gene.
getProfilesDataSingleGene()getProfilesDataSingleGene()
dataframe with profiles data for a single gene
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Select Case from Breast Cancer ENV <- new.env(parent = emptyenv()) ENV$curselectCases <- 9 ##Select Genetic Profile from Breast Cancer ENV$curselectGenProfs <- 4 ## get Specific Mutation data for 73 Genes list ## Not run: getProfilesDataSingleGene() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Select Case from Breast Cancer ENV <- new.env(parent = emptyenv()) ENV$curselectCases <- 9 ##Select Genetic Profile from Breast Cancer ENV$curselectGenProfs <- 4 ## get Specific Mutation data for 73 Genes list ## Not run: getProfilesDataSingleGene() ## End(Not run)
get specific Mutation data for multiple genes
getSpecificMut()getSpecificMut()
a a dataframe with specific mutation informations
readRDS(paste(path.package("canceR"),"/extdata/rdata//ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getSpecificMut() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata//ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: getSpecificMut() ## End(Not run)
get Summary results from GSEA-R (Broad Institute)
getSummaryGSEA()getSummaryGSEA()
Dataframe with summary results
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: Run.GSEA() getSummaryGSEA() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: Run.GSEA() getSummaryGSEA() ## End(Not run)
Survival plot
getSurvival(Coxph)getSurvival(Coxph)
Coxph |
if Coxph = 0 : plot Kaplan-Meier curves else Coxph= 1 : plot Cox Proportional Hazard Model |
Survival plot
surv <- 11 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) getSurvival(Coxph = 1) ## End(Not run)surv <- 11 ## Not run: readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) getSurvival(Coxph = 1) ## End(Not run)
get text in tcltk windows
getTextWin(text)getTextWin(text)
text |
string |
tcltk windows with text
text <- "mytext" ## Not run: getTextWin(text) ## End(Not run)text <- "mytext" ## Not run: getTextWin(text) ## End(Not run)
See http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/R-GSEA_Readme
GSEA
Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273)
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/R-GSEA_Readme
GSEA.Analyze.Sets(directory,topgs="",non.interactive.run= FALSE,height=12,width=17)GSEA.Analyze.Sets(directory,topgs="",non.interactive.run= FALSE,height=12,width=17)
directory |
|
topgs |
|
non.interactive.run |
|
height |
|
width |
|
GSEA.Analyze.Sets
Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273)
http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page.
## Not run: ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.ConsPlot
GSEA.ConsPlot(V, col.names, main = " ", sub = " ", xlab = " ", ylab = " ")GSEA.ConsPlot(V, col.names, main = " ", sub = " ", xlab = " ", ylab = " ")
V |
|
col.names |
|
main |
|
sub |
|
xlab |
|
ylab |
|
GSEA.ConsPlot
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.EnrichmentScore
GSEA.EnrichmentScore(gene.list, gene.set, weighted.score.type = 1, correl.vector = NULL)GSEA.EnrichmentScore(gene.list, gene.set, weighted.score.type = 1, correl.vector = NULL)
gene.list |
|
gene.set |
|
weighted.score.type |
|
correl.vector |
GSEA.EnrichmentScore
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.EnrichmentScore2
GSEA.EnrichmentScore2(gene.list, gene.set, weighted.score.type = 1, correl.vector = NULL)GSEA.EnrichmentScore2(gene.list, gene.set, weighted.score.type = 1, correl.vector = NULL)
gene.list |
|
gene.set |
|
weighted.score.type |
|
correl.vector |
GSEA.EnrichmentScore2
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.Gct2Frame
GSEA.Gct2Frame(filename = "NULL")GSEA.Gct2Frame(filename = "NULL")
filename |
GSEA.GCT2Frame
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.Gct2Frame2
GSEA.Gct2Frame2(filename = "NULL")GSEA.Gct2Frame2(filename = "NULL")
filename |
GSEA.GCT2Frame2
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.GeneRanking
A |
|
class.labels |
|
gene.labels |
|
nperm |
|
permutation.type |
|
sigma.correction |
|
fraction |
|
replace |
|
reverse.sign |
GSEA.GeneRanking
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.HeatMapPlot
GSEA.HeatMapPlot
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.HeatMapPlot2
GSEA.HeatMapPlot2
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.NormalizeCols
GSEA.NormalizeCols(V)GSEA.NormalizeCols(V)
V |
GSEA.NormalizeCols
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ## Load workspace ##Run.GSEA() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ## Load workspace ##Run.GSEA() ## End(Not run)
GSEA.NormalizeRows
GSEA.NormalizeRows(V)GSEA.NormalizeRows(V)
V |
GSEA.NormalizeRows
## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)## Not run: library(canceR) ## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ##Run.GSEA() ## End(Not run)
GSEA.ReadClsFile
GSEA.ReadClsFile(file = "NULL")GSEA.ReadClsFile(file = "NULL")
file |
GSEA.ReadClsFile
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)
GSEA.Res2Frame
GSEA.Res2Frame(filename = "NULL")GSEA.Res2Frame(filename = "NULL")
filename |
GSEA.NormalizeCols
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)
GSEA.Threshold
GSEA.Threshold(V, thres, ceil)GSEA.Threshold(V, thres, ceil)
V |
|
thres |
|
ceil |
GSEA.Threshold
## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)
GSEA.VarFilter
GSEA.VarFilter(V, fold, delta, gene.names = "NULL")GSEA.VarFilter(V, fold, delta, gene.names = "NULL")
V |
|
fold |
|
delta |
|
gene.names |
GSEA.VarFilter
## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)
GSEA.write.gct
GSEA.write.gct(gct, filename)GSEA.write.gct(gct, filename)
gct |
|
filename |
GSEA.Write.gct
## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)## Load workspace readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)
Search MSigDb that overlap gene list
Match_GeneList_MSigDBMatch_GeneList_MSigDB
GeneList
readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: Match_GeneList_MSigDB() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/prad_michPhenoTest1021.rds", sep="")) ## Not run: Match_GeneList_MSigDB() ## End(Not run)
Dialog box to specify Gene Symbol.
modalDialog(title, question, entryInit, entryWidth = 40,returnValOnCancel = "ID_CANCEL")modalDialog(title, question, entryInit, entryWidth = 40,returnValOnCancel = "ID_CANCEL")
title |
string |
question |
string |
entryInit |
entryInit |
entryWidth |
40 |
returnValOnCancel |
"ID_CANCEL" |
dialog box
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Select Case from Breast Cancer ENV <- new.env(parent = emptyenv()) ENV$curselectCases <- 9 ##Select Genetic Profile from Breast Cancer ENV$curselectGenProfs <- 4 ## get Specific Mutation data for 73 Genes list ## Not run: getProfilesDataSingleGene() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Select Case from Breast Cancer ENV <- new.env(parent = emptyenv()) ENV$curselectCases <- 9 ##Select Genetic Profile from Breast Cancer ENV$curselectGenProfs <- 4 ## get Specific Mutation data for 73 Genes list ## Not run: getProfilesDataSingleGene() ## End(Not run)
Global environment to store canceR variables.
The format is: <environment: 0xb3eb240>
myGlobalEnv <- new.env(parent = emptyenv())myGlobalEnv <- new.env(parent = emptyenv())
OLD.GSEA.EnrichmentScore
gene.list |
|
gene.set |
OLD.GSEA.EnchmentScore
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: ##Run.GSEA() ## End(Not run)
Plotting two genetic profiles for one Gene
plot_1Gene_2GenProfs()plot_1Gene_2GenProfs()
plot
readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) ## Not run: plot_1Gene_2GenProfs() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) ## Not run: plot_1Gene_2GenProfs() ## End(Not run)
plot correlation of two genes expressions.
plot_2Genes_1GenProf()plot_2Genes_1GenProf()
plot
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: plot_2Genes_1GenProf() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: plot_2Genes_1GenProf() ## End(Not run)
model plotting with tcltk
plotModel(plotCommand, title= "TITLE",hscale=1, vscale=1 )plotModel(plotCommand, title= "TITLE",hscale=1, vscale=1 )
plotCommand |
plotcommand |
title |
title of plot |
hscale |
horizintal scale |
vscale |
vertical scale |
plot
readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) ## Not run: plot_1Gene_2GenProfs() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/gbm_tcgaPlotTwoGenProf.rds", sep="")) ## Not run: plot_1Gene_2GenProfs() ## End(Not run)
bind non equal row
rbind.na(..., deparse.level = 1)rbind.na(..., deparse.level = 1)
... |
(generalized) vectors or matrices. |
deparse.level |
integer controlling the construction of labels in the case of non-matrix-like arguments (for the default method): deparse.level = 0 constructs no labels; the default, deparse.level = 1 or 2 constructs labels from the argument names. |
a data frame with merged rows
## Not run: row1 <- c("a","b","c","d") row2 <- c("A", "B", "C") row3 <- rbind.na(row1, row2) ## End(Not run)## Not run: row1 <- c("a","b","c","d") row2 <- c("A", "B", "C") row3 <- rbind.na(row1, row2) ## End(Not run)
The main function to run GSEA-R from Broad Institute
Run.GSEA()Run.GSEA()
A vector with sampling size
readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: Run.GSEA() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/ucec_tcga_pubGSEA1021.rds", sep="")) ## Not run: Run.GSEA() ## End(Not run)
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()setWorkspace()
paths of output files
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: setWorkspace() ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: setWorkspace() ## End(Not run)
S3 method to test cBioPortal connection
## S3 method for class 'CGDS' test(x, ...)## S3 method for class 'CGDS' test(x, ...)
x |
connection object |
... |
not used |
Testing checked appropriate Cases for appropriate Genetic profiles.
testCheckedCaseGenProf(singleGene=0)testCheckedCaseGenProf(singleGene=0)
singleGene |
specify if the check for querying genetic profile for a specific gene or not (0,1). |
dialog box with warning message
readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: testCheckedCaseGenProf(singleGene=0) ## End(Not run)readRDS(paste(path.package("canceR"),"/extdata/rdata/brca_tcga73genes.rds", sep="")) ## Not run: testCheckedCaseGenProf(singleGene=0) ## End(Not run)
Unify row names in data frame with the same order of gene list.
UnifyRowNames(x,geneList)UnifyRowNames(x,geneList)
x |
data frame with gene symbol in the row name |
geneList |
a gene list |
a data frame having the gene in row name ordered as in gene list.
cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)cgds <- cBioPortal( hostname = "www.cbioportal.org", protocol = "https", api = "/api/v2/api-docs" ) ## Not run: getDataByGenes( api = cgds, studyId = "gbm_tcga_pub", genes = c("NF1", "TP53", "ABL1"), by = "hugoGeneSymbol", molecularProfileIds = "gbm_tcga_pub_mrna" ) ## End(Not run)