4 Main Window
After selecting studies and pressing on Get Cases and Genetic Profiles Button, the main window appears (Figure~@ref(fig:mainWindow.png)) and displays the progress of loading data of selected studies. The Main Window has a Toolbar with Menus (see following paragraphs). It is subdivised in two columns. The first column lists Cases for all selected studies. The first line of every study indicates its Index and its short description. The remain lines enumerate Cases with short description of data type and the number of samples. The second list box shows selected Cases. Similarly, the second column displays informations of Genetic Profiles.
User can select a single or multiple lines with attention to correspond the Case with appropriate Genetic Profile.
(#fig:mainWindow.png) Main Window of canceR package. 1, Toolbar, 2, list box of loaded Cases; 3, list box of selected Cases; 4, list box of loaded Genetic Profiles; 5, list box of selected Genetic Profiles
4.1 Gene List
The first step to get genomics data is to specify what are interesting genes for user. The Gene List button browses folders to load Gene list file or displays examples of genes list. The genes could be in text file (.txt) with one gene by line using HUGO gene Symbol. The function removes automatically duplicate genes.
4.2 Clinical Data
The Multiple Cases button displays successively selected Cases. Results are returned in a table with row for each case and a column for each clinical attribute (Figure 4B). User could select all or some clinical data by checking dialog box (Figure 4A). For example, we select clinical attributes:
Overall Survival months: Overall survival, in months.
Overall Survival Status: Overall survival status, usually indicated as
LIVINGorDECEASED.Disease Free Survival months: Disease free survival, in months.
Disease Free Survival status: Disease free survival status, usually indicated as
DiseaseFreeorRecurred/Progressed.Age at diagnosis: Age at diagnosis.
(#fig:clinicalData.png) Getting clinical data for Breast Invasive Carcinoma. A, Dialog Check Box to select clinical data; B, Results of quering clinical data of Breast Invasive Carcinoma (TCGA, Nature 2012)
4.3 Mutation
User can search all mutation in gene list of all selected studies. He needs to select All tumors samples in Cases and Mutations in gentics profiles to get mutations (Figure~@ref(fig:Mutation1.png)).
(#fig:Mutation1.png) Selection Mutation Cases
Mutation function allows user to select about 15 informations corresponding to mutations (Figure~1A). The results is a table with rows for each sample/case, and columns corresponding to the informations cheched in dialog mutation check box (Figure~1B).
Figure 1: Select Clinical data with Mutation
User can filter mutation result only for specific amino acid change (Figure~@ref(fig:specificMutation.png)).
(#fig:specificMutation.png) Specific Mutation
4.4 Methylation
User can search gene methylation and its correlation with mRNA expression. User needs to select Cases and Genetic Profiles with same methylation assay (HM450 or HM27) for the same study. Multiple Cases selection is allowed for one gene list (Figure~@ref(fig:methylation.png)).
(#fig:methylation.png) Selecting methylation data
The dialog box of methylation function allows user to specify the threshold of the correlation rate (Figure~@ref(fig:Met_rate)A). cBioportal~(Cerami et al. 2012, @Gao2013) includes only methylation data from the probe with the strongest negative correlation between the methylation signal and the gene’s expression. The result table (Figure~@ref(fig:Met_rate)B) lists genes with median of rate upper than 0.8.
(#fig:Met_rate) A, Methylation dialog box; B, Methylation results. Correlation of silensing gene expression by methylation (HM27) with correlation rate r > 0.8 for gene list in Breast Invasive Carcinoma (TCGA, Nature 2012).
4.5 Profiles
The function get Profile Data depends on gene list, cases, and genetic profiles. If a Single gene option is done, dialog box appears to specify gene symbol (Figure~@ref(fig:singleProfile.png)). The returned dialog check box allows user to choose some/all profiles data (Figure~@ref(fig:singleProfile.png)B). The result (table) lists some/all genetic profiles data in columns (CNA, Met, Mut, mRNA,RPPA) and all available samples in rows (Figure~@ref(fig:singleProfile.png)C). Oppositely, if Multiple genes option is done, the returned table displays genes expression for gene list (column) for all samples (rows). In the case of multiple genes, the tables are saved in Results/ProfilesData folder (Figure~@ref(fig:multipleProfiles.png)).