Default gene expression module data

Gene expression module data from Chaussabel et al. (2008) and Li et al. (2014)

Details

The tmod package includes one data set of class tmod which can be loaded with data(tmod). This data set is derived from two studies (see package vignette for details). By default, enrichment analysis with tmod uses this data set; however, it is not loaded into user workspace by default.

References

Chaussabel, Damien, Charles Quinn, Jing Shen, Pinakeen Patel, Casey Glaser, Nicole Baldwin, Dorothee Stichweh, et al. 2008. "A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus." Immunity 29(1):150-64.

Li, Shuzhao, Nadine Rouphael, Sai Duraisingham, Sandra Romero-Steiner, Scott Presnell, Carl Davis, Daniel S Schmidt, et al. 2014. "Molecular Signatures of Antibody Responses Derived from a Systems Biology Study of Five Human Vaccines." Nature Immunology 15(2):195-204.

See also

tmod-class, modmetabo

Examples

# list of first 10 modules
data(tmod)
tmod
#> An object of class "tmodGS"
#> 	606 gene sets, 12712 genes
tmod$MODULES[1:10, ]
#> NULL
tmod[1:10]
#> An object of class "tmodGS"
#> 	10 gene sets, 455 genes