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

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Documentation for package ‘coMET’ version 1.20.0

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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)
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 [obselete]
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
otherRegulatoryRegionsBiomart_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 [obselete]
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