KnowYourCG (Supervised Learning of Sparse DNA Methylome Data)

Install knowYourCG

Release version can be installed from Bioconductor

BiocManager::install("knowYourCG")

Development version can be installed from github.

BiocManager::install('zhou-lab/knowYourCG')

Main Functions

Enrichment Testing

• testEnrichment - Test for enrichment of query in knowledgebase sets
• testEnrichment2 - Test enrichment from YAME-compressed CG sets
• testEnrichmentSEA - GSEA-like test for association of categorical variable against continuous variable
• testProbeProximity - Test if query probes share closer genomic proximity than random
• aggregateTestEnrichments - Aggregate test enrichment results

Database Management

• getDBs - Get databases by full or partial names
• listDBGroups - List database group names
• loadDBs - Load knowledgebase databases from TSV files
• buildGeneDBs - Build gene-probe association database
• dbStats - Aggregate methylation over database set features
• annoProbes - Annotate Probe IDs using KYCG databases

Visualization

• KYCG_plotBar - Bar plot of most enriched CG groups
• KYCG_plotDot - Dot plot of most enriched CG groups
• KYCG_plotEnrichAll - Plot enrichment test results
• KYCG_plotLollipop - Lollipop plot of log(estimate)
• KYCG_plotManhattan - Manhattan plot for EWAS results
• KYCG_plotMeta - Plot meta gene or other meta genomic features
• KYCG_plotMetaEnrichment - Plot meta gene enrichment
• KYCG_plotPointRange - Point range plot for enrichment results
• KYCG_plotSetEnrichment - Plot set enrichment
• KYCG_plotVolcano - Volcano plot of -log2(p.value) vs log(estimate)
• KYCG_plotWaterfall - Waterfall plot of log(estimate)

Data Access

• kycgDataCache - Cache KnowYourCG data
• kycgDataGet - Get KnowYourCG data

Utilities

• linkProbesToProximalGenes - Find genes in genomic proximity to Infinium probes
• bedToCg - Convert BED CpG set to YAME .cg format

See also

https://github.com/zhou-lab/YAME