tmod

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:

• “panel plot” visualizations which allow to compare results of gene set enrichments;
• several enrichment algorithms are implemented in tmod, in particular the very efficient, versatile and reproducible algorithm called “CERNO”;
• it includes a library of gene sets derived from clustering of gene expression data from human blood, which is especially useful in functional analysis in infection and immune responses.

Installation

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")

Tmod manual

• Access the documentation using vignette("tmod")
• Full user manual is found here

Example usage

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