about |
about canceR |
canceR |
main function |
canceRHelp |
canceR Help |
canceR_Vignette |
open pdf vignette |
cbind.na |
bind non equal colunm |
ClinicalData |
ClinicalData |
dialogGeneClassifier |
Dialogue Box for gene classifier setting: sample size and postprob threshold |
dialoggetGeneListMSigDB |
Multi-select choice of gene sets from loaded MSigDB |
dialogMetOption |
Dialog Box to set methylation options |
dialogMut |
Dialog bos to set returned Mutation information |
dialogOptionCircos |
Checkbox to select dimensions |
dialogOptionGSEAlm |
Dialogbox to select variables from Clinical data |
dialogOptionPhenoTest |
Checkbox to select variables from clinical data |
dialogPlotOption_SkinCor |
Checkbox to select variables for plotting |
dialogSamplingGSEA |
Dialog Box for Sampling patients from expression profile data used for GSEA-R (Broad Institute) |
dialogSelectFiles_GSEA |
Dialog Box to Select GCT, CLS, GMT and output Files for GSEA-R (Broad Institute) |
dialogSpecificMut |
dialog box to Specify Mutation using Regular Expression. Search specific mutation using regular expression. |
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). |
displayInTable |
Display matrix in tcltk table |
GeneExpMatrix |
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. |
getCasesGenProfs |
get Cases and Genetic Profiles of selected Studies. |
getCircos |
get Circos Layout for selected studies and selected dimensions |
getClinicalDataMatrix |
get matrix with clinical from file |
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. |
getCor_ExpCNAMet |
Get gene correlation for multiple dimensions. |
geteSet |
Built Expression Set (eSet) from profile data. |
getGCTCLSExample |
get GCT and CLS example files. |
getGCT_CLSfiles |
get Profile (GCT file) and Phenotype (CLS file) Data from Disease. |
getGeneExpMatrix |
get matrix with gene expression from file |
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. |
getGeneListExample |
get Gene List from examples. User can select one from available gene list |
getGeneListFromMSigDB |
get gene list from MSigDB |
getGenesClassifier |
get Genes Classifier |
getGenesTree_MultipleCases |
Get successively trees of genes list for multiple cases |
getGenesTree_SingleCase |
classify genes in tree for two phenotypes in the same case(disease). |
getGenProfs |
Get Genetic Profile from selected Studies |
getGSEAlm_Diseases |
get GSEA linear modeling by studies (diseases) |
getGSEAlm_Variables |
get GSEA linear modeling by variables (phenotype) |
getInTable |
get dataframe in TK/TCL table |
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. |
getMegaProfData |
Get profile data for more than 500 genes list. |
getMetDataMultipleGenes |
get Methylation data for multiple genes |
getMSigDB |
Reduce MSigDB size for only gene list |
getMSigDBExample |
get example of .gmt file from MSigDB (Broad Institute) |
getMSigDBfile |
Dialog Box to Select MSigDB Files from drive |
getMutData |
get Mutation data for multiple genes |
getPhenoTest |
Associate phenotype to Studies (cancers) |
getProfilesDataMultipleGenes |
get Profles Data of multiple genes |
getProfilesDataSingleGene |
get Profiles Data for a Single Gene. |
getSpecificMut |
get specific Mutation data for multiple genes |
getSummaryGSEA |
get Summary results from GSEA-R (Broad Institute) |
getSurvival |
Survival plot |
getTextWin |
get text in tcltk windows |
GSEA |
GSEA-R (Broad Institute) |
GSEA.Analyze.Sets |
GSEA.Analyze.Sets |
GSEA.ConsPlot |
GSEA.ConsPlot |
GSEA.EnrichmentScore |
GSEA.EnrichmentScore |
GSEA.EnrichmentScore2 |
GSEA.EnrichmentScore2 |
GSEA.Gct2Frame |
GSEA.Gct2Frame |
GSEA.Gct2Frame2 |
GSEA.Gct2Frame2 |
GSEA.GeneRanking |
GSEA.GeneRanking |
GSEA.HeatMapPlot |
GSEA.HeatMapPlot |
GSEA.HeatMapPlot2 |
GSEA.HeatMapPlot2 |
GSEA.NormalizeCols |
GSEA.NormalizeCols |
GSEA.NormalizeRows |
GSEA.NormalizeRows |
GSEA.ReadClsFile |
GSEA.ReadClsFile |
GSEA.Res2Frame |
GSEA.Res2Frame |
GSEA.Threshold |
GSEA.Threshold |
GSEA.VarFilter |
GSEA.VarFilter |
GSEA.write.gct |
GSEA.write.gct |
Match_GeneList_MSigDB |
Search MSigDb that overlap gene list |
modalDialog |
Dialog box to specify Gene Symbol. |
myGlobalEnv |
myGlobalEnv |
OLD.GSEA.EnrichmentScore |
OLD.GSEA.EnrichmentScore |
plotModel |
model plotting with tcltk |
plot_1Gene_2GenProfs |
Plotting two genetic profiles for one Gene |
plot_2Genes_1GenProf |
plot correlation of two genes expressions. |
rbind.na |
bind non equal row |
Run.GSEA |
The main function to run GSEA-R from Broad Institute |
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. |
testCheckedCaseGenProf |
Testing checked appropriate Cases for appropriate Genetic profiles. |