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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.