# Interactive Multi-Omics Cancers Data Visualization and Analysis

## Documentation for package ‘bioCancer’ version 1.39.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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