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

## Documentation for package ‘coMET’ version 1.0.0

- 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)
chromatinHMMAll | Creating multiple chromHMM tracks from the UCSC genome browser
chromatinHMMOne | Creating one chromHMM track from the UCSC genome browser
chrUCSC2ENSEMBL | Removing "chr" to the chromosome number from UCSC to transform it to ENSEMBL chromosome format
ClinVarCnvTrack | Create one track of the genomic positions of variants from the ClinVar database (CNV only)
ClinVarMainTrack | 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
CoreillCNVTrack | Create one track of the genomic positions of CNV in chromosomal aberration and inherited disorders from the NIGMS Human Genetic Cell Repository data
COSMICTrack | Create one track of the genomic positions of variants from COSMIC
cpgIslandsUCSC | create track CpG Island from UCSC
DNAseUCSC | Creation of an UCSC's DNase clusters track
GADTrack | Create one track of the genomic positions of variants from the Genetic Association Database (GAD)
gcContent | Create one track of GC content from UCSC
GeneReviewsTrack | Create one track of the genomic positions of variants from GeneReviews
genesENSEMBL | Create one track of the genes in the genomic regions of interest from EMSEMBL
genesNameENSEMBL | Obtain the genes names in the genomic regions of interest from ENSEMBL
GWASTrack | Create one track of the genomic positions of variants from the GWAS catalog
HistoneAll | Create multiple tracks of histone modifications from the UCSC genome browser
HistoneOne | Create one track of one histone modification profile from the UCSC genome browser
ISCATrack | Create one track of the genomic positions of variants from ISCA
knownGenesUCSC | Create a track of known genes from the UCSC genome browser
regulationBiomart | Create a regulation track from ENSEMBL
RepeatMaskerTrack | Create one track of the genomic positions of regions from RepeatMaskerTrack
snpBiomart | Create a short variation track from ENSEMBL
snpLocationsUCSC | Create a SNP track from UCSC
structureBiomart | Create a structural variation track from ENSEMBL
transcriptENSEMBL | Create a track of transcripts from ENSEMBL