SampleData: Sample Data for coGPS

In coGPS: cancer outlier Gene Profile Sets

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.

coGPS documentation built on Nov. 8, 2020, 11:11 p.m.