Functional analysis of DNA methylome datasets

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Documentation for package ‘knowYourCG’ version 1.3.1

• 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)
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 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