cn.mat {MVisAGe}

DNA copy number data from 98 head and neck squamous cell carcinoma (HNSC) patients

Description

Quantitative gene-level DNA copy number measurements for 98 samples from The Cancer Genome Atlas (TCGA) HNSC cohort. The all_data_by_genes.txt dataset from the GISTIC2 output was restricted to the first 100 columns and genes that lie on chromosomes 11 and 12. Genes appear in rows; samples appear in columns (other than the first two columns described below). Gene symbols are used as row names and sample identifiers are used as column names (other than the first two columns).

Usage

cn.mat

Format

A matrix with 2719 rows and 100 columns

Locus.ID

gene identifier

Cytoband

cytoband containing the gene of interest

Remaining Columns

quantitative DNA copy number

Column names

sample identifiers (other than the first two columns)

Row names

gene symbols

Source

https://gdac.broadinstitute.org/