npc: Example data set

In wiscstatman/Rolemodel: Gene-set analysis via MFA

Description

NPC data set.

Usage

data(npc)

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

Sengupta et al. (2006) reported a genome-wide expression study of nasopharyngeal car- cinoma (NPC), with particular attention paid to unusually extensive negative associations between host genes in the NPC cells and the expression of a key gene in the infecting Epstein- Barr virus (EBV). Genes showing extreme negative Spearman correlation were entered onto the gene list; fully 438 genes (Entrez ID) constituted the 5% FDR-controlled list. We integrated this list with GO[5:50], 5994 GO terms that hold between 5 and 50 human genes. GO[5:50] itself annotates only about half of the human genes (10293), and only 232 of the genes showing NPC-EBV association.

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).

Examples

data(npc)

str(npc$I)
str(npc$y)

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