OncoScape is a package for gene prioritization in the R statistical programming environment. The analysis is run in a contrast fashion, i.e. always two groups of samples are compared with each other. Examples include:

• tumors vs. normals
• cell lines vs. normals
• treatment responders vs resistant
• samples with mutations in gene X vs wild type

Currently, analyses of five data types are implemented in OncoScape:

1. gene expression
2. DNA copy number
3. DNA methylation
4. mutation
5. shRNA knock-down data

Aberrations in each gene are called for each data type separately and scored as 0 (no aberration found) or 1 (aberration found). These scores are summed across data types to give the final score. OncoScape differentiates between activating (oncogene-like) and inactivating (tumor suppressor-like) aberrations and calculates independent scores for both directions. It is possible to run the analysis on any combination of these data types.

The analysis proceeds in four steps: 0. data import

1. calculate statistics (using "do*Analysis" methods)
2. filtering and scoring (using "summarize*" methods)
3. plotting of results

Example scripts for putting everything together are:

• TCGA_PAN/SCRIPTS/load_tcga_pancancer_data.r
• TCGA_PAN/SCRIPTS/prioritize_tcga_step1.r
• TCGA_PAN/SCRIPTS/prioritize_tcga_step2.r
• TCGA_PAN/SCRIPTS/plot*

• achilles.r: functions to analyze data from Project Achilles (http://www.broadinstitute.org/achilles)
• cnamap.r: functions to analyze copy number data
• compare.r: functions for comparing OncoMap results from two different runs
• expression.r: functions to analyze gene expression data
• methylationmap.r: functions to analyze DNA methylation data
• plotting.r: functions for plotting results
• preprocessTCGA.r: functions for preprocessing data from the TCGA pancancer project
• scoring.r: functions for calculating final scores
• sommut.r: functions to analyze somatic mutation data
• survival.r: functions to analyze survival data (not used at the moment)
• tcga_synapse.r: functions to download TCGA data from Sage Bionetwork's Synapse (www.synapse.org)
• uploadResutlsSynapse.r: functions to upload result files to Synapse
• utils.r: helper functions used by others in this project