ctd: Comparative Toxicogenomics Database

In tpq/miSciTools: Miscellaneous Science Tools for Bioinformatic Analysis

Description

These data catalog chemical-gene interactions curated from the literature. Each interaction in this database contains useful information about the source of this knowledge and the type of interaction observed.

Usage

data(ctd)

Format

A data.frame with >1,000,000 chemical-gene interactions (rows) and 11 annotations (columns). Retrieved on April 9, 2019.

Source

http://ctdbase.org/reports/CTD_chem_gene_ixns.csv.gz

Examples

## Not run: 
library(miSciTools)
data(ctd)
head(ctd[, c("GeneID", "ChemicalName")])
genes <- ctd$GeneID[ctd$ChemicalName == "Platinum"]
pvals <-
  simpliGSEA(genes = genes, # Test "Platinum" interactions
             universe = unique(ctd$GeneID),
             annot.genes = ctd$GeneID,
             annot.terms = ctd$ChemicalName)
head(sort(p.adjust(pvals)))

## End(Not run)

tpq/miSciTools documentation built on Sept. 16, 2019, 4:43 p.m.