Functional analysis of DNA methylome datasets

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Documentation for package ‘knowYourCG’ version 1.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

aggregateTestEnrichments	Aggregate test enrichment results
annoProbes	Annotate Probe IDs using KYCG databases
buildGeneDBs	build gene-probe association database
dbStats	dbStats aggregates methylation of a given betas matrix over specified database set features
getDBs	Get databases by full or partial names of the database group(s)
listDBGroups	List database group names
testEnrichment	testEnrichment tests for the enrichment of a set of probes (query set) in a number of features (database sets).
testEnrichmentFisher	testEnrichmentFisher uses Fisher's exact test to estimate the association between two categorical variables.
testEnrichmentSEA	uses the GSEA-like test to estimate the association of a categorical variable against a continuous variable.
testEnrichmentSpearman	testEnrichmentSpearman uses the Spearman statistical test to estimate the association between two continuous variables.
testGO	tests Gene Ontology of genes overlapping CpG query
testProbeProximity	testProbeProximity tests if a query set of probes share closer genomic proximity than if randomly distributed