In Su-informatics-lab/DIStudio: Drug Informatics Studio

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

First, we load the DIStudio package and load the default data model:

library(DIStudio)

model <- loadDefaultModel()

Next, suppose we're interested in Alzheimer's Disease (AD) drugs. We can lookup related nodes:

listNodes(model, name="alzheimer")

The list can also be filtered to include only diseases:

listNodes(model, name="alzheimer", kind=DISEASE_KIND)

From here, we have the code for Alzheimer's Disease: C904. To find drugs related to AD, use the listRelatedDrugs function:

drugs <- listRelatedDrugs(model, "C904")
nrow(drugs)
head(drugs)

To lookup annotations related to one of these drugs, use the listDrugAnnotations function:

annotations <- listDrugAnnotations(model, "C14004")
nrow(annotations)
head(annotations)

The list can be restricted to specific annotation kinds:

listDrugAnnotations(model, "C14004", kinds=MECHANISM_OF_ACTION_KIND)

Drug similarity can be calculated with the Similarity function:

Similarity(model, c("C14004", "C13950"), "C14954")

Finally, the model can be visualized with the viewModel function. The entire default model is too large to be meaningfully graphed, but the getDataSubmodel function can extract a portion of the model containing only a subset of nodes:

codes <- c(drugs$code, annotations$code)
submodel <- getDataSubmodel(model, codes)

viewModel(submodel)

Su-informatics-lab/DIStudio documentation built on May 5, 2020, 10:33 p.m.