In charlieccarey/monarchr: Interface to Monarch Initiative API for Phenotype Ontology and Genotype

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

GOAL: show homologs, diseases, phenotypes, anatomy, pathways and interactions associated with a gene.

We demonstrate these associations which correspond to tabs from Monarch Initiative website that result from a search at the website for the human gene NCBIGene:8314.

Loading monarchr client library and libraries for displaying tables.

(DT is the datatables package which we use to display the results. knitr includes kable, another way to generate tables.)

library(monarchr)
library(DT)
library(knitr)
gene <- "NCBIGene:8314"

Get the homologs (paralogs, orthologs and homologs) to a gene.

Homologs of gene, displayed using DataTable.

homs <- bioentity_homologs(gene)
datatable(homs$homologs)

Get the diseases associated with a gene.

Diseases associated with gene, displayed using kable.

Note, the publications look clickable, but are not. This is a bug in the formatting. They are meant to be raw text.

dis <- bioentity_diseases_assoc_w_gene(gene)
kable(dis$diseases)

Get the phenotypes associated with a gene.

Phenotypes associated with gene, displayed using kable.

Note, the publications look clickable, but are not. This is a bug in the formatting. They are meant to be raw text.

phe <- bioentity_phenotypes_assoc_w_gene(gene)
kable(head(phe$phenotypes))

Get the anatomy associated with a gene.

Anatomy associated with gene, displayed using kable.

Molecularly defined by expression data?

anat <- bioentity_exp_anatomy_assoc_w_gene(gene)
kable(head(anat$anatomy))

Get the pathways associated with a gene.

Pathways associated with gene, displayed using kable.

pth <- bioentity_pathways_assoc_w_gene(gene)
kable(pth$pathways)

Get the interactions associated with a gene.

Interactions associated with gene, displayed using kable.

Note, the publications look clickable, but are not. This is a bug in the formatting. They are meant to be raw text.

intx <- bioentity_interactions_assoc_w_gene(gene)
kable(head(intx$interactions))

charlieccarey/monarchr documentation built on Dec. 12, 2023, 12:57 p.m.