Tmod is a suite of gene set enrichment algorithms, visualizations and utilities which comes bundled with a few libraries of gene sets (“modules”). Following features distinguish tmod from other packages:
You can install the released version of tmod from CRAN with:
install.packages("tmod")And the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("january3/tmod")vignette("tmod")library(tmod)
#> For tmod user guide, type `vignette("tmod")`
data(EgambiaResults)
tt <- EgambiaResults
## gene set enrichment analysis
res <- tmodCERNOtest(tt$GENE_SYMBOL)
head(res)
#> ID Title cerno N1 AUC
#> LI.M37.0 LI.M37.0 immune activation - generic cluster 426.3578 100 0.7462103
#> DC.M4.2 DC.M4.2 Inflammation 151.1520 20 0.9503953
#> DC.M3.4 DC.M3.4 Interferon 129.4727 17 0.8315780
#> DC.M1.2 DC.M1.2 Interferon 112.7056 17 0.9004196
#> DC.M7.29 DC.M7.29 Undetermined 118.6759 20 0.8087599
#> LI.M11.0 LI.M11.0 enriched in monocytes (II) 113.8086 20 0.7766542
#> cES P.Value adj.P.Val
#> LI.M37.0 2.131789 1.824844e-18 1.105856e-15
#> DC.M4.2 3.778799 8.040039e-15 2.436132e-12
#> DC.M3.4 3.808019 4.609405e-13 9.310998e-11
#> DC.M1.2 3.314869 2.298170e-10 3.481728e-08
#> DC.M7.29 2.966897 1.002268e-09 1.214749e-07
#> LI.M11.0 2.845216 5.255069e-09 5.307620e-07