brca: BRCA gene expression dataset as SummarizedExperiment

In hipathia: HiPathia: High-throughput Pathway Analysis

Description

A dataset containing a matrix with the Gene expression of 40 samples from the BRCA-US project from The Cancer Genome Atlas (TCGA), and their experimental design, containing 20 "Tumor" samples 20 "Normal" samples.

Usage

data(brca)

Format

SummarizedExperiment. The assay is a matrix with 40 columns and 18638 rows. Row names are Entrez IDs and column names are the TCGA identifyers of the samples. The colData() is a data.frame with 1 column and 40 rows, including the experimental design of the 40 samples from the BRCA-US project from TCGA. Field group is the type of sample, either "Tumor" or "Normal".

Details

The gene expression matrix includes 40 samples. The data has been log-transformed and normalized with TMM.

Value

SummarizedExperiment including a matrix with 40 columns and 18638 rows. Row names are Entrez IDs and column names are the TCGA identifyers of the samples.

Source

https://cancergenome.nih.gov/

hipathia documentation built on Nov. 8, 2020, 7:52 p.m.