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

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Documentation for package ‘coMET’ version 1.0.0

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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