t2d: Example data set

In wiscstatman/Rolemodel: Gene-set analysis via MFA

Description

Type 2 diabetes data set.

Usage

data(t2d)

Format

It's a list of an incidence matrix I and the corresponding gene-level data y. The incidence matrix is a 0-1 matrix with unique row and column names, where rows are genes and columns are gene-sets. Gene-level data y is a 0-1 vector with the same names as the row names of I.

Details

From a large-scale genome-wide association study (GWAS) involving more than 34,000 cases and 114,000 control subjects, 77 human genes have been implicated as affecting T2D disease susceptibility (see reference). To assess the functional content of this gene list, we extracted 6037 gene ontology terms, each annotating between 5 and 50 genes. These 6037 terms annotate a total of 10,626 genes; among the 77 T2D-associated genes, 58 are in this moderately annotated class.

References

Zhishi W., Qiuling H., Bret L. and Michael N.: A multi-functional analyzer uses parameter constaints to improve the efficiency of model-based gene-set analysis (2013).

Andrew P. M. and others: Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes (2012). Nature Genetics, Volume 44-9.

Examples

data(t2d)

str(t2d$I)
str(t2d$y)

wiscstatman/Rolemodel documentation built on May 4, 2019, 6:32 a.m.