coGPS (version 1.16.0)

SampleData: Sample Data for coGPS

Description

Here we present an example of coGPS analysis.

Arguments

Exon_exprs_matched

Expression data for 44 tumors and 25 normals. Each row indicates a gene with row name showing gene name and each column indicates a sample with column name showing sample name.

Exon_class_matched

A length 69 vector showing status of corresponding exon samples, 0 for normals and 1 for tumors.

Methy_exprs_matched

Methylation data for 44 tumors and 25 normals.

Methy_class_matched

A length 69 vector showing status of corresponding methylation samples, 0 for normals and 1 for tumors.

CNV_exprs_matched

Copy number data for 44 tumors and 25 normals.

CNV_class_matched

A length 69 vector showing status of corresponding copy number samples, 0 for normals and 1 for tumors.

Hs.gmtl.c1

Broad Institute C1 Positional Gene Sets.

Details

In this application, the columns of each data type are matched. In other words, the first columns of Exon_exprs_matched, Methy_exprs_matched and CNV_exprs_matched correspond to the same patient. And hence the Exon_class_matched, Methy_class_matched and CNV_class_matched are identical. However, suppose in applications that we are not concerned with the outlier gene list for each patient, we can leave with the samples (columns) unmatched.