Functional analysis of DNA methylome datasets

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Documentation for package ‘knowYourCG’ version 1.7.11

• 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
bedToCg	Convert BED CpG set to YAME .cg format
buildGeneDBs	build gene-probe association database
dbStats	dbStats aggregates methylation of a given betas matrix over specified database set features
df_master	Master data frame for all object to cache
getDBs	Get databases by full or partial names of the database group(s)
kycgDataCache	Cache KnowYourCG data
kycgDataGet	Get KnowYourCG data
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
linkProbesToProximalGenes	find genes in genomic proximity to given Infinium probes
listDBGroups	List database group names
loadDBs	Load knowledgebase databases from TSV files
testEnrichment	Test for enrichment of query in knowledgebase sets
testEnrichment2	Test enrichment from YAME-compressed CG sets
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.
testProbeProximity	testProbeProximity tests if a query set of probes share closer genomic proximity than if randomly distributed