tmod
Feature Set Enrichment Analysis for Metabolomics and Transcriptomics
Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis. See Zyla et al (2019)
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