Interactive Multi-Omics Cancers Data Visualization and Analysis
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Documentation for package ‘bioCancer’ version 1.32.0
Help Pages
| -package | Launch bioCancer with default browser |
| .dbEscapeString | Private Escape string |
| .getTableName | Gets the table name from the INPARANOID style genus names. |
| .pickRef | Secret function that does the magic for pickRefSeq. |
| AnnotationFuncs | Annotation translation functions |
| attriColorGene | Attribute Color to Gene |
| attriColorValue | Attribute Color to Value |
| attriColorVector | Attribute color to a vector of numeric values |
| attriShape2Gene | Attribute shape to nodes |
| attriShape2Node | Attributes shape to Nodes |
| bioCancer | Launch bioCancer with default browser |
| CGDS | CGDS connect object to cBioPortal |
| checkDimensions | Check wich Cases and genetic profiles are available for selected study |
| coffeewheel | This is an htmlwidgets-based visualization tool for hierarchical data. It is zoomable, meaning that you can interact with the hierarchy and zoom in/out accordingly. |
| coffeewheelOutput | Widget output function for use in Shiny |
| displayTable | Display dataframe in table using DT package |
| Edges_Diseases_obj | get Edges dataframe for Gene/Disease association from geNetClassifier |
| epiGenomics | Default dataset of bioCancer |
| findPhantom | Check if PhantomJS is installed. Similar to webshot |
| getEvidenceCodes | Returns GO evidence codes. |
| getFreqMutData | get mutation frequency |
| getGenesClassification | get genes classification |
| getListProfData | get list of data frame with profiles data (CNA,mRNA, Methylation, Mutation...) |
| getList_Cases | get list of cases of each selected study in Classifier panel |
| getList_GenProfs | get list of genetic profiles of each selected study in Classifier panel |
| getOrthologs | Performs quicker lookup for orthologs in homologe data packages |
| getProfData | search and get genetic profiles (CNA,mRNA, Methylation, Mutation...) |
| getSequensed_SampleSize | get samples size of sequensed genes |
| mapLists | Replaces contents of list A with elements of list B |
| metabologram | Circular plot of hierarchital data of genetic profile. |
| metabologramOutput | Widget output function for use in Shiny |
| Mutation_obj | Atribute mutation frequency to nodes |
| Node_df_FreqIn | Attributes size to Nodes depending on number of interaction |
| Node_Diseases_obj | Attributes color and shape to Nodes of Diseases |
| Node_obj_CNA_ProfData | Attribute CNA data to node border |
| Node_obj_FreqIn | Attribute interaction frequency to node size |
| Node_obj_Met_ProfData | Attribute gene Methylation to Nodes |
| Node_obj_mRNA_Classifier | Atrribute genes expression to color nodes |
| pickGO | Cleans up result from org.Xx.egGO and returns specific GO identifiers |
| pickRefSeq | Picks a prioritised RefSeq identifier from a list of identifiers |
| removeNAs | Removes entries equal 'NA' from list or vector |
| renderCoffeewheel | Widget render function for use in Shiny |
| renderMetabologram | Widget render function for use in Shiny |
| reStrColorGene | Restructure the list of color attributed to the genes in every dimenssion for every studies |
| reStrDimension | Restructure the list of color attributed to the genes in every study for every dimensions |
| reStrDisease | Restructure the list of color attributed to the genes in every disease |
| returnTextAreaInput | Return message when the filter formula is not correct (mRNA > 500) |
| Studies_obj | get object for grViz. Link Studies to genes |
| switchButton | A function to change the Original checkbox of rshiny into a nice true/false or on/off switch button No javascript involved. Only CSS code. |
| test.CGDS | S3 method to test cBioPortal connection |
| translate | Translate between different identifiers |
| UnifyRowNames | Unify row names in data frame with the same order of gene list. |
| user_CNA | Example of Copy Number Alteration (CNA) dataset |
| user_MetHM27 | Example of Methylation HM27 dataset |
| user_MetHM450 | Example of Methylation HM450 dataset |
| user_mRNA | Example of mRNA expression dataset |
| user_Mut | Example of Mutation dataset |
| whichGeneList | Verify which gene list is selected |
| widgetThumbnail | Capture html output widget as .png in R |