# coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

## Documentation for package ‘coMET’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

coMET-package | visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns (and also for other omic-WAS)
bindingMotifsBiomart_ENSEMBL | Creates a binding motif track from ENSEMBL
ChIPTF_ENCODE | Creates a TF motif track from ENCODE
chromatinHMMAll_UCSC | Creating multiple chromHMM tracks from the UCSC genome browser
chromatinHMMOne_UCSC | Creating one chromHMM track from the UCSC genome browser
chromHMM_RoadMap | Creates a ChromHMM track from a file of RoadMap
chrUCSC2ENSEMBL | Removing "chr" to the chromosome number from UCSC to transform it to ENSEMBL chromosome format
ClinVarCnv_UCSC | Create one track of the genomic positions of variants from the ClinVar database (CNV only)
ClinVarMain_UCSC | Create one track of the genomic positions of variants from the ClinVar database (variants only)
coMET | visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns (and also for other omic-WAS)
comet | Visualize EWAS results in a genomic region of interest
comet.list | List the correlations between omic features
comet.web | Visualize EWAS results in a genomic region of interest with predefined annotation tracks
CoreillCNV_UCSC | Create one track of the genomic positions of CNV in chromosomal aberration and inherited disorders from the NIGMS Human Genetic Cell Repository data
COSMIC_UCSC | Create one track of the genomic positions of variants from COSMIC
cpgIslands_UCSC | create track CpG Island from UCSC
dgfootprints_RoadMap | Creates a track of DNA motif positional bias in digital genomic Footprinting Sites (DGFP) from a file of RoadMap
DNaseI_FANTOM | Creates a enhancer/promoter track from FANTOM
DNaseI_RoadMap | Creates a promoter/enhancer regions track from a file of RoadMap
DNAse_UCSC | Creation of an UCSC's DNase clusters track
eQTL | Creates a track from a file for eQTL data
eQTL_GTEx | Creates a eQTL track from GTEx
GAD_UCSC | Create one track of the genomic positions of variants from the Genetic Association Database (GAD)
gcContent_UCSC | Create one track of GC content from UCSC
GeneReviews_UCSC | Create one track of the genomic positions of variants from GeneReviews
genesName_ENSEMBL | Obtain the genes names in the genomic regions of interest from ENSEMBL
genes_ENSEMBL | Create one track of the genes in the genomic regions of interest from EMSEMBL
GWAScatalog_UCSC | Create one track of the genomic positions of variants from the GWAS catalog
HiCdata2matrix | Creates a HiC matrix from a file (Rao et al., 2014)
HistoneAll_UCSC | Create multiple tracks of histone modifications from the UCSC genome browser
HistoneOne_UCSC | Create one track of one histone modification profile from the UCSC genome browser
imprintedGenes_GTEx | Creates a imprinted genes track from GTEx
interestGenes_ENSEMBL | Create one track of the genes in the genomic regions of interest from EMSEMBL
interestTranscript_ENSEMBL | Create a track of transcripts from ENSEMBL
ISCA_UCSC | Create one track of the genomic positions of variants from ISCA (obselete database)
knownGenes_UCSC | Create a track of known genes from the UCSC genome browser
metQTL | Creates a track from a file for metQTL data
miRNATargetRegionsBiomart_ENSEMBL | Creates a track of miRNA target regions from ENSEMBL
otherRegulatoryRegions_ENSEMBL | Creates a track of other regulatory regions from ENSEMBL
psiQTL_GTEx | Creates a psiQTL track from GTEx
refGenes_UCSC | Create a track of RefSeq genes from the UCSC genome browser
regulationBiomart_ENSEMBL | Create a regulation track from ENSEMBL
regulatoryEvidenceBiomart_ENSEMBL | Creates a regulatory feature track from ENSEMBL
regulatoryFeaturesBiomart_ENSEMBL | Creates a regulatory feature track from ENSEMBL
regulatorySegmentsBiomart_ENSEMBL | Creates a binding motif track from ENSEMBL
repeatMasker_UCSC | Create one track of the genomic positions of regions from repeatMasker_UCSC
segmentalDups_UCSC | Create one track of the genomic positions of regions from segmentalDups_UCSC
snpBiomart_ENSEMBL | Create a short variation track from ENSEMBL
snpLocations_UCSC | Create a SNP track from UCSC
structureBiomart_ENSEMBL | Create a structural variation track from ENSEMBL
TFBS_FANTOM | Creates a TFBS motif track from FANTOM
transcript_ENSEMBL | Create a track of transcripts from ENSEMBL