# Functional analysis of DNA methylome datasets

## Documentation for package ‘knowYourCG’ version 1.4.0

- 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 query in knowledgebase sets
testEnrichment2 | Test enrichment from YAME-compressed CG 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