This package is in early development.

Introduction.

This is the README for the monarchr package.

We use monarchr to retrieve and work with genetic, phenotype, and ontological information from the Monarch Inititiative monarchinitiative.org.

Monarch Initiative’s API provides structured data from many biological databases. Some of the key advantages of Monarch ensue from their considerable effort to enable cross species lookups and unification of many different, often species specific ontologies.

The monarchr package has the following goals:

1. Query Monarch’s web API, returning R objects for further analysis in R.
2. Ease access from other popular bioconductor packages to Monarch’s data.
3. Facilitate reuse of Monarch’s data by other packages.

view documentation

view code

Also see the swagger codegen autogenerated client to the api

Installation

install.packages("devtools")
devtools::install_github("charlieccarey/monarchr")

Example: Get homologs to a particular gene.

Often, we are interested in a particular gene’s homologs or orthologs in another organisms.

We query Monarch by using the bioentity_homologs function.

library(monarchr)
gene <- "NCBIGene:8314"
results <- bioentity_homologs(gene)

The results are a list comprised of:

• A tibble of homologs (paralogs, orthologs and homologs).
• A response object (for troubleshooting and to access the raw response headers and json content if necessary)

When we ran this query, we retrieved 17 homologs.

library(DT)
datatable(results$homologs)

More info and Troubleshooting.

See troubleshooting and other articles in documentation.

The troubleshooting article demonstrates how to verify that our homologs match the results given at Monarch Initiative’s website.