Query and Analyse the 'EWAS Atlas' Database

Provides a client for the 'EWAS Atlas' web services (< https://ngdc.cncb.ac.cn/ewas/>; Li et al. (2019) ), allowing users to query epigenome-wide association study (EWAS) data by CpG (cytosine-phosphate-guanine) probe identifier, gene symbol, or genomic region, and to run trait, Gene Ontology, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, and genomic location enrichment analyses on a set of CpG probes. Query functions support concurrent, rate-limited requests to the remote service. Results are returned as tidy data frames with dedicated summary and plotting methods, including word clouds of enriched 'EWAS Atlas' trait terms.

EWAScaller

EWAScaller is an R client for the EWAS Atlas database. It queries CpG probes, gene symbols, and genomic regions for epigenome-wide association study (EWAS) results, runs trait/GO/KEGG/genomic-location enrichment analyses on probe sets, and provides plotting helpers including word clouds of enriched trait terms.

Installation

# install.packages("remotes")
remotes::install_github("SAADAT-Abu/EWAScaller")

Usage

Query by CpG probe, gene, or genomic region

library(EWAScaller)

cpg_res <- query_cpg(c("cg05575921", "cg11903855", "cg00240195"))
summary(cpg_res)
head(cpg_res$associations)

gene_res <- query_gene("AHRR")
region_res <- query_region(chr = "5", start = 373000, end = 374000)

All three query functions dispatch requests across a small worker pool (workers) and pause delay seconds between batches, so large probe lists can be resolved faster without overwhelming the remote service.

Enrichment analysis

data(example_cpgs)
probes <- unique(example_cpgs$query_cpg)

enr <- ewas_enrichment(probes, background = "850K",
                        types = c("trait", "genomic_location", "gene_ontology", "kegg"))
summary(enr)
top_traits(enr)

Plots

plot_wordcloud(cpg_res)
plot_wordcloud(enr, type = "trait")

autoplot(cpg_res, type = "traits")
autoplot(cpg_res, type = "chromosome")
autoplot(cpg_res, type = "direction")
autoplot(enr, type = "trait")

Data source

EWAScaller queries the EWAS Atlas REST and toolkit web services (https://ngdc.cncb.ac.cn/ewas/api). Please cite the EWAS Atlas when using data retrieved through this package.

License

MIT