Functional analysis of DNA methylome datasets

Documentation for package ‘knowYourCG’ version 1.2.5

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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)
KYCG_plotBar	Bar plot to show most enriched CG groups from testEnrichment
KYCG_plotDot	Dot plot to show most enriched CG groups from testEnrichment
KYCG_plotEnrichAll	plot enrichment test result
KYCG_plotLollipop	creates a lollipop plot of log(estimate) given data with fields estimate.
KYCG_plotManhattan	KYCG_plotManhattan makes a manhattan plot to summarize EWAS results
KYCG_plotMeta	Plot meta gene or other meta genomic features
KYCG_plotMetaEnrichment	Plot meta gene or other meta genomic features
KYCG_plotPointRange	Plot point range for a list of enrichment testing results against the same set of databases
KYCG_plotSetEnrichment	Plot Set Enrichment
KYCG_plotVolcano	creates a volcano plot of -log2(p.value) and log(estimate) given data with fields estimate and p.value.
KYCG_plotWaterfall	create a waterfall plot of log(estimate) given test enrichment
listDBGroups	List database group names
testEnrichment	testEnrichment tests for the enrichment of query in knowledgebase 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