Functional analysis of DNA methylome datasets


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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