RichR

RichR: Enrichment for Diseases in a Set of Genes

It provides a list of genes associated to diseases (g2d$clean and g2d$complete) based on the following 4 publications (GS2D, Fontaine (2016) [doi:10.18547/gcb.2016.vol2.iss1.e33], DisGeNET, Pinero (2016) [doi:10.1093/nar/gkw943] Berto2016, Berto (2016) [doi:10.3389/fgene.2016.00031] and PsyGeNET, Sacristan (2015) [doi:10.1093/bioinformatics/btv301]). Those lists were combined and manually curated to have matching disease names. When provided a list of gene names, it calculates the disease enrichment of the gene set. The enrichment is calculated using proportion test and Fisher’s exact test. Adjusted fdr p-values are returned alongside with p-values combined using the Fisher’s method.

You can download the package from CRAN using:

install.packages('RichR')

Input data

The input data for RichR are: the Background, that is the list of genes to be used as background control, the Genes2Dis, a data.frame containing genes and association to phenotypes and disorders and Genes, a vector of genes that should be tested for enrichment.

We recommend using g2d$clean as Genes2Dis. This is a manually curated list of genes and association to disorders.

Usage

data('g2d')

g2d_clean = g2d$clean

The user can choose a particular disorder, or use the whole disease set to compare to

g2d_ASD = subset(g2d_clean, g2d_clean$Disease %in% c('AUTISM'))

Enrichment(Background = g2d_clean$Gene.symbol,

Genes2Dis = g2d_ASD,Genes = g2d_ASD$Gene.symbol[1:100])