data_n_code/breast_cancer/README.md

In huynguyen250896/DrGA: DrGA: driver gene analysis in an automatic manner

Description

Breast cancer data are downloaded from the cBioPortal for Cancer Genomics (http://www.cbioportal.org) [1], including somatic mutation (n = 2,369), EXP (n = 1,904), and CNA (n = 2,173). It contains the METABRIC breast cancer cohort assembled from 2509 primary breast cancer patients with 548 matched normals in the United Kingdom and Canada [2].

The files here contain: 1. Link_to_download_full_data.txt: A text file has a shared google drive link to download all the raw data mentioned.

1. raw_data.zip: a subset of raw data necessary for running examples, extracted from the full one above.

2. process_data_DrGA.R: R code examples to process the raw data from scratch before inputting them to DrGA.

3. processed_DrGA.RData: Processed data are available to run DrGA immediately.

4. output_BRCA: Gained results from running DrGA.

Reference

1. Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404. https://doi.org/10.1158/2159-8290.cd-12-0095 (2012).

2. Pereira, B. et al. The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes. Nat. Commun. 7, 11479. https://doi.org/10.1038/ncomms11479 (2016).

huynguyen250896/DrGA documentation built on Oct. 18, 2023, 5:47 a.m.