cnvs: TCGA breast invasive carcinoma (BRCA) copy number gistic2...

In shunsambongi/sambcdata: Select TCGA Breast Cancer datasets

Description

TCGA breast invasive carcinoma (BRCA) thresholded gene-level copy number variation (CNV) estimated using the GISTIC2 method.

Usage

cnvs

Format

An untidy dataframe with genes as rows and samples as columns (25,777 identifiers X 1080 samples).

Details

Copy number profile was measured experimentally using whole genome microarray at a TCGA genome characterization center. Subsequently, GISTIC2 method was applied using the TCGA FIREHOSE pipeline to produce gene-level copy number estimates. GISTIC2 further thresholded the estimated values to -2,-1,0,1,2, representing homozygous deletion, single copy deletion, diploid normal copy, low-level copy number amplification, or high-level copy number amplification. Genes are mapped onto the human genome coordinates using UCSC xena HUGO probeMap. Reference to GISTIC2 method PMID:21527027.

shunsambongi/sambcdata documentation built on May 24, 2019, 5:05 a.m.