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

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Documentation for package ‘coMET’ version 1.40.0

• 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)
col2HSV	col2HSV: converts a color to HSV in hexadecimal notation
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
complementary	Complementary or opposite color
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 - obselete function
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
opposite	Complementary or opposite color
otherRegulatoryRegionsBiomart_ENSEMBL	Creates a track of other regulatory regions from ENSEMBL
pizza	Pizza color wheel
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
setColors	Set Colors for a color wheel
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