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

Visualisation of EWAS results in a genomic region. In addition to phenotype-association P-values, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. It can be used to other omic-wide association scans as long as the data can be translated to genomic level and for any species.

AuthorTiphaine C. Martin, Thomas Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T. Bell
Date of publicationNone
MaintainerTiphaine Martin <tiphaine.martin@kcl.ac.uk>
LicenseGPL (>= 2)
Version1.6.0
http://epigen.kcl.ac.uk/comet

View on Bioconductor

Man pages

bindingMotifsBiomart_ENSEMBL: Creates a binding motif track from ENSEMBL

check.configVar: Check if all variables have a value related to the functions...

check.configVar.cometlist: Check if all variables have a value related to the function...

check.format.mydata: Check the format of different data

ChIPTF_ENCODE: Creates a TF motif track from ENCODE

chromatinHMMAll_UCSC: Creating multiple chromHMM tracks from the UCSC genome...

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...

ClinVarCnv_UCSC: Create one track of the genomic positions of variants from...

ClinVarMain_UCSC: Create one track of the genomic positions of variants from...

comet: Visualize EWAS results in a genomic region of interest

comet.list: List the correlations between omic features

coMET-package: visualisation of regional epigenome-wide association scan...

comet.web: Visualize EWAS results in a genomic region of interest with...

compute.cormatrix: Compute the correlation matrix between CpG sites

CoreillCNV_UCSC: Create one track of the genomic positions of CNV in...

COSMIC_UCSC: Create one track of the genomic positions of variants from...

cpgIslands_UCSC: create track CpG Island from UCSC

cpgPvalue: Create a plot of pvalue of CpG with DataTrack of Gviz

create.color.bar: Create color bar of heatmap

create.color.list: Create color list for the main data

create.color.list.large: Create list of colors for the supplementary data

createList.trackUser: Create list of Gviz's tracks from user's data

create.symbol.list: create symbol list for the upper plot in the grid

create.symbol.list.large: Create a list of symblo for the supplementary data

create.tracks.user: Create track from the user data

create.tracks.web: Create tracks for the web page (see cometweb)

datasets: Data sets

dgfootprints_RoadMap: Creates a track of DNA motif positional bias in digital...

DNaseI_FANTOM: Creates a enhancer/promoter track from FANTOM

DNaseI_RoadMap: Creates a promoter/enhancer regions track from a file of...

DNAse_UCSC: Creation of an UCSC's DNase clusters track

draw.legend: Display the legend of the plot

draw.name.genes.web: display the gene names

draw.name.tracks.web: Display names of tracks for web page(see cometweb)

draw.plot.annotation: Display the annotation track from ENSEMBL and UCSC

draw.plot.axis.data: Display the axis data of plot of pvalue

draw.plot.comet: Display the three plots of coMET

draw.plot.comet.nopval: Display the three plots of coMET

draw.plot.comet.web: Display the three plots of coMET for the web version

draw.plot.cormatrix.plot: Display the correlation plot at the bottom of the grid

draw.plot.grid.mydata: Display a plot of pvalue of data from MYDATA.FILE

draw.plot.grid.mydata.large: Display the plot of pvalue of the supplementary data

draw.plot.grid.mydata.names: Display the name of elements defined in DATA.FILE

draw.plot.grid.setup: Set up the grid of plot

draw.plot.linesconnection: Display the connector lines for the probes

draw.plot.mydata.ggbio: plot tracks created by ggbio that you want to visualise

eQTL: Creates a track from a file for eQTL data

eQTL_GTEx: Creates a eQTL track from GTEx

fix.values: Fix and update the values of variables related to main data

fix.values.generic: Fix and update the values of generic variables

fix.values.large: Fix and update the values of supplementary data

GAD_UCSC: Create one track of the genomic positions of variants from...

gcContent_UCSC: Create one track of GC content from UCSC

GeneReviews_UCSC: Create one track of the genomic positions of variants from...

genes_ENSEMBL: Create one track of the genes in the genomic regions of...

genesName_ENSEMBL: Obtain the genes names in the genomic regions of interest...

GWAScatalog_UCSC: Create one track of the genomic positions of variants from...

HiCdata2matrix: Creates a HiC matrix from a file (Rao et al., 2014)

HistoneAll_UCSC: Create multiple tracks of histone modifications from the UCSC...

HistoneOne_UCSC: Create one track of one histone modification profile from the...

imprintedGenes_GTEx: Creates a imprinted genes track from GTEx

interestGenes_ENSEMBL: Create one track of the genes in the genomic regions of...

interestTranscript_ENSEMBL: Create a track of transcripts from ENSEMBL

ISCA_UCSC: Create one track of the genomic positions of variants from...

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

printPlot.comet: Create the plot on file from coMet function

printPlot.comet.nopval: Create the plot on file from coMet function

printPlot.comet.web: Display the plot from cometWeb funciton

psiQTL_GTEx: Creates a psiQTL track from GTEx

read.config: Extract the values of variables from configuration file

read.file.cormatrix: Read, compute and extract the values from correlation matrix...

read.file.mydata: Read the files of main data and extract data

read.file.mydata.large: Read the files of supplemantary data and extract data

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...

retrieve.data: Retrieve the data from configuration file and data files

segmentalDups_UCSC: Create one track of the genomic positions of regions from...

set.image.parameters: Set up the parameters of image

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

xenorefGenes_UCSC: Create a track for xeno-reference genes from the UCSC genome...

Files in this package

coMET/DESCRIPTION
coMET/LICENSE
coMET/NAMESPACE
coMET/NEWS
coMET/R
coMET/R/AnalyseFile.R coMET/R/BiofeatureGraphics.R coMET/R/DrawPlot.R coMET/R/GeneralMethodComet.R coMET/R/comet.R coMET/R/cometWeb.R coMET/R/cometlist.R
coMET/README.md
coMET/build
coMET/build/vignette.rds
coMET/data
coMET/data/BindingMotifAll.rda
coMET/data/BindingMotifMultiple.rda
coMET/data/BindingMotifSingle.rda
coMET/data/ClinVarCnvTrack.rda
coMET/data/CoreillCNVTrack.rda
coMET/data/DNaseI_RoadMapSingle.rda
coMET/data/DupTrack.rda
coMET/data/GWASTrack.rda
coMET/data/GeneReviewTrack.rda
coMET/data/GeneReviewsTrack.rda
coMET/data/ISCAtrack.rda
coMET/data/ISCAtrack_Grch38.rda
coMET/data/OtherRegulatoryRegionsAll.rda
coMET/data/OtherRegulatoryRegionsSingle.rda
coMET/data/PancreasIG.rda
coMET/data/PancreasIGtrack.rda
coMET/data/PancreasimprintedIG.rda
coMET/data/PancreasimprintedIGtrack.rda
coMET/data/RegulatoryEvidenceBiomartAll.rda
coMET/data/RegulatoryEvidenceBiomartMultiple.rda
coMET/data/RegulatoryEvidenceBiomartSingle.rda
coMET/data/RegulatoryFeaturesBiomartAll.rda
coMET/data/RegulatoryFeaturesBiomartMultiple.rda
coMET/data/RegulatoryFeaturesBiomartSingle.rda
coMET/data/RegulatorySegmentsBiomartAll.rda
coMET/data/RegulatorySegmentsBiomartMultiple.rda
coMET/data/RegulatorySegmentsBiomartSingle.rda
coMET/data/SegmentalDupsUCSC.rda
coMET/data/StomachIG.rda
coMET/data/StomachIGtrack.rda
coMET/data/allIG.rda
coMET/data/allIGtrack.rda
coMET/data/allimprintedIG.rda
coMET/data/allimprintedIGtrack.rda
coMET/data/bindMotifsBiomartTrackAll.rda
coMET/data/bindMotifsBiomartTrackMultiple.rda
coMET/data/bindMotifsBiomartTrackSingle.rda
coMET/data/bindingMotifsBiomartAll.rda
coMET/data/bindingMotifsBiomartMultiple.rda
coMET/data/bindingMotifsBiomartSingle.rda
coMET/data/chipTFtrack.rda
coMET/data/chipTFtrack_old.rda
coMET/data/chromHMM_RoadMapAll.rda
coMET/data/chromHMM_RoadMapAllE063.rda
coMET/data/chromHMM_RoadMapMultiple.rda
coMET/data/chromHMM_RoadMapSingle.rda
coMET/data/chromatinHMMRoadMapAll.rda
coMET/data/chromatinHMMRoadMapMultiple.rda
coMET/data/chromatinHMMRoadMapSingle.rda
coMET/data/chromhmmNoPattern.rda
coMET/data/chromhmmPattern.rda
coMET/data/chromhmmtrackone.rda
coMET/data/clinVarMaintrack.rda
coMET/data/coreilVarianttrack.rda
coMET/data/cosmicVarianttrack.rda
coMET/data/cpgIslandsUCSC.rda
coMET/data/cpgIslandtrack.rda
coMET/data/datalist
coMET/data/dgfootprints_RoadMapSingle.rda
coMET/data/dnasetrack.rda
coMET/data/dyaRM.rda
coMET/data/dyaRMtrack.rda
coMET/data/eGTexTrackSNP.rda
coMET/data/eGTexTrackall.rda
coMET/data/eQTLAll.rda
coMET/data/eQTLMultiple.rda
coMET/data/eQTLSingle.rda
coMET/data/eQTLTrackAll.rda
coMET/data/eQTLTrackMultiple.rda
coMET/data/eQTLTrackSingle.rda
coMET/data/enhFANTOMtrack.rda
coMET/data/enhRM.rda
coMET/data/enhRMtrack.rda
coMET/data/gadtrack.rda
coMET/data/gcContent.rda
coMET/data/gctrack.rda
coMET/data/geneENSEMBLtrack.rda
coMET/data/geneNameEnsembl.rda
coMET/data/genesENSEMBL.rda
coMET/data/genesGencodetrack.rda
coMET/data/genesNameENSEMBL.rda
coMET/data/genesUcsctrack.rda
coMET/data/genetrack4RM.rda
coMET/data/genetrack4psiGTEX.rda
coMET/data/grtrack4eGTex.rda
coMET/data/histonalltrack.rda
coMET/data/histoneonetrack.rda
coMET/data/imprintedGenesGTEx.rda
coMET/data/interestGenesENSEMBL.rda
coMET/data/interestTranscriptENSEMBL.rda
coMET/data/interestgenesENSMBLtrack.rda
coMET/data/interesttransENSMBLtrack.rda
coMET/data/knownGenesUCSC.rda
coMET/data/matrix_HiC_Rao.rda
coMET/data/metQTLSingle.rda
coMET/data/metQTLTrackAll.rda
coMET/data/metQTLTrackMultiple.rda
coMET/data/metQTLTrackSingle.rda
coMET/data/miRNATargetRegionsBiomart.rda
coMET/data/miRNATargetRegionsBiomartTrack.rda
coMET/data/otherRegulatoryRegionsTrackAll.rda
coMET/data/otherRegulatoryRegionsTrackSingle.rda
coMET/data/promRMtrack.rda
coMET/data/promRMtrackE063.rda
coMET/data/psiGTex.rda
coMET/data/psiGTexTrackSNP.rda
coMET/data/psiGTexTrackall.rda
coMET/data/refGenesUCSC.rda
coMET/data/regulationENSEMBLtrack.rda
coMET/data/regulatoryEvidenceBiomartTrackAll.rda
coMET/data/regulatoryEvidenceBiomartTrackMultiple.rda
coMET/data/regulatoryEvidenceBiomartTrackSingle.rda
coMET/data/regulatoryFeaturesBiomartTrackAll.rda
coMET/data/regulatoryFeaturesBiomartTrackMultiple.rda
coMET/data/regulatoryFeaturesBiomartTrackSingle.rda
coMET/data/regulatorySegmentsBiomartTrackAll.rda
coMET/data/regulatorySegmentsBiomartTrackMultiple.rda
coMET/data/regulatorySegmentsBiomartTrackSingle.rda
coMET/data/repeatMaskerTrack.rda
coMET/data/snpBiomart.rda
coMET/data/snpBiomarttrack.rda
coMET/data/snpUCSCtrack.rda
coMET/data/snptrack.rda
coMET/data/strucBiomarttrack.rda
coMET/data/structureBiomart.rda
coMET/data/tfbsFANTOMtrack.rda
coMET/data/transENSMBLtrack.rda
coMET/data/xenogenestrack.rda
coMET/data/xenorefGenesUCSC.rda
coMET/inst
coMET/inst/CITATION
coMET/inst/doc
coMET/inst/doc/coMET.R
coMET/inst/doc/coMET.Rnw
coMET/inst/doc/coMET.pdf
coMET/inst/extdata
coMET/inst/extdata/JpegTables
coMET/inst/extdata/JpegTables/BindingMotifsBiomart.jpg
coMET/inst/extdata/JpegTables/ChromHMM.jpg
coMET/inst/extdata/JpegTables/ChromHMM_UCSC.jpg
coMET/inst/extdata/JpegTables/ChromHMM_coMET.jpg
coMET/inst/extdata/JpegTables/ISCATrack.jpg
coMET/inst/extdata/JpegTables/ISCATrack_old.jpg
coMET/inst/extdata/JpegTables/OtherRegulatoryRegions.jpg
coMET/inst/extdata/JpegTables/RegulatoryElementsENSEMBL.jpg
coMET/inst/extdata/JpegTables/RegulatoryEvidence_1.jpg
coMET/inst/extdata/JpegTables/RegulatoryEvidence_2.jpg
coMET/inst/extdata/JpegTables/RegulatoryEvidence_3.jpg
coMET/inst/extdata/JpegTables/RegulatoryFeaturesBiomart.jpg
coMET/inst/extdata/JpegTables/RegulatorySegmentsBiomart.jpg
coMET/inst/extdata/JpegTables/RoadMap15_RoadMap.jpg
coMET/inst/extdata/JpegTables/RoadMap18_RoadMap.jpg
coMET/inst/extdata/JpegTables/RoadMap18_coMET.jpg
coMET/inst/extdata/JpegTables/RoadMap25_RoadMap.jpg
coMET/inst/extdata/JpegTables/RoadMap25_coMET.jpg
coMET/inst/extdata/JpegTables/bindingMotifBiomart.jpg
coMET/inst/extdata/JpegTables/eQTL.jpg
coMET/inst/extdata/JpegTables/metQTL.jpg
coMET/inst/extdata/JpegTables/structureBiomart.jpg
coMET/inst/extdata/config_cyp1b1_zoom.txt
coMET/inst/extdata/config_cyp1b1_zoom_4comet.txt
coMET/inst/extdata/config_cyp1b1_zoom_4cometnopval.txt
coMET/inst/extdata/config_cyp1b1_zoom_4cometnopval_Grch38.txt
coMET/inst/extdata/config_cyp1b1_zoom_4nomatrix.txt
coMET/inst/extdata/config_cyp1b1_zoom_4nomatrix_Grch38.txt
coMET/inst/extdata/config_cyp1b1_zoom_4webserver.txt
coMET/inst/extdata/config_cyp1b1_zoom_4webserver_Grch38.txt
coMET/inst/extdata/config_gata55_larger_article.txt
coMET/inst/extdata/config_gata55_larger_article_rev.txt
coMET/inst/extdata/cyp1b1_infofile.bed
coMET/inst/extdata/cyp1b1_infofile.txt
coMET/inst/extdata/cyp1b1_infofile_Grch38.txt
coMET/inst/extdata/cyp1b1_infofile_bed.txt
coMET/inst/extdata/cyp1b1_infofile_bed_v2.bed
coMET/inst/extdata/cyp1b1_infofile_bed_v2.txt
coMET/inst/extdata/cyp1b1_infofile_bed_v2_hg38.bed
coMET/inst/extdata/cyp1b1_infofile_bed_v3.bed
coMET/inst/extdata/cyp1b1_infofile_bed_v3.txt
coMET/inst/extdata/cyp1b1_infofile_bed_v3_hg38.bed
coMET/inst/extdata/cyp1b1_infofile_exprGene_region.txt
coMET/inst/extdata/cyp1b1_infofile_exprGene_region_Grch38.txt
coMET/inst/extdata/cyp1b1_infofile_exprGene_region_v2.csv
coMET/inst/extdata/cyp1b1_res37_cormatrix_list_BH05.txt
coMET/inst/extdata/cyp1b1_res37_rawMatrix.txt
coMET/inst/extdata/cyp1b1_zoom_plus_name_expr.pdf
coMET/inst/extdata/datalist
coMET/inst/extdata/gata4_55probes_info.txt
coMET/inst/extdata/gata4_55probes_rawMatrix.txt
coMET/inst/extdata/gata4_55probes_residuals.txt
coMET/inst/extdata/gata4_95probes_info.txt
coMET/inst/extdata/gata_comet_55probes_large_article.eps
coMET/inst/extdata/gata_comet_55probes_large_article_gene.eps
coMET/inst/extdata/gata_comet_55probes_large_article_rev.eps
coMET/inst/unitTests
coMET/inst/unitTests/ChangeLog.txt
coMET/inst/unitTests/Citation.txt
coMET/inst/unitTests/test_chrUCSC2ENSEMBL.R
coMET/man
coMET/man/COSMIC_UCSC.Rd coMET/man/ChIPTF_ENCODE.Rd coMET/man/ClinVarCnv_UCSC.Rd coMET/man/ClinVarMain_UCSC.Rd coMET/man/CoreillCNV_UCSC.Rd coMET/man/DNAse_UCSC.Rd coMET/man/DNaseI_FANTOM.Rd coMET/man/DNaseI_RoadMap.Rd coMET/man/GAD_UCSC.Rd coMET/man/GWAScatalog_UCSC.Rd coMET/man/GeneReviews_UCSC.Rd coMET/man/HiCdata2matrix.Rd coMET/man/HistoneAll_UCSC.Rd coMET/man/HistoneOne_UCSC.Rd coMET/man/ISCA_UCSC.Rd coMET/man/TFBS_FANTOM.Rd coMET/man/bindingMotifsBiomart_ENSEMBL.Rd coMET/man/check.configVar.Rd coMET/man/check.configVar.cometlist.Rd coMET/man/check.format.mydata.Rd coMET/man/chrUCSC2ENSEMBL.Rd coMET/man/chromHMM_RoadMap.Rd coMET/man/chromatinHMMAll_UCSC.Rd coMET/man/chromatinHMMOne_UCSC.Rd coMET/man/coMET-package.Rd coMET/man/comet.Rd coMET/man/comet.list.Rd coMET/man/comet.web.Rd coMET/man/compute.cormatrix.Rd coMET/man/cpgIslands_UCSC.Rd coMET/man/cpgPvalue.Rd coMET/man/create.color.bar.Rd coMET/man/create.color.list.Rd coMET/man/create.color.list.large.Rd coMET/man/create.symbol.list.Rd coMET/man/create.symbol.list.large.Rd coMET/man/create.tracks.user.Rd coMET/man/create.tracks.web.Rd coMET/man/createList.trackUser.Rd coMET/man/datasets.Rd coMET/man/dgfootprints_RoadMap.Rd coMET/man/draw.legend.Rd coMET/man/draw.name.genes.web.Rd coMET/man/draw.name.tracks.web.Rd coMET/man/draw.plot.annotation.Rd coMET/man/draw.plot.axis.data.Rd coMET/man/draw.plot.comet.Rd coMET/man/draw.plot.comet.nopval.Rd coMET/man/draw.plot.comet.web.Rd coMET/man/draw.plot.cormatrix.plot.Rd coMET/man/draw.plot.grid.mydata.Rd coMET/man/draw.plot.grid.mydata.large.Rd coMET/man/draw.plot.grid.mydata.names.Rd coMET/man/draw.plot.grid.setup.Rd coMET/man/draw.plot.linesconnection.Rd coMET/man/draw.plot.mydata.ggbio.Rd coMET/man/eQTL.Rd coMET/man/eQTL_GTEx.Rd coMET/man/fix.values.Rd coMET/man/fix.values.generic.Rd coMET/man/fix.values.large.Rd coMET/man/gcContent_UCSC.Rd coMET/man/genesName_ENSEMBL.Rd coMET/man/genes_ENSEMBL.Rd coMET/man/imprintedGenes_GTEx.Rd coMET/man/interestGenes_ENSEMBL.Rd coMET/man/interestTranscript_ENSEMBL.Rd coMET/man/knownGenes_UCSC.Rd coMET/man/metQTL.Rd coMET/man/miRNATargetRegionsBiomart_ENSEMBL.Rd coMET/man/otherRegulatoryRegionsBiomart_ENSEMBL.Rd coMET/man/printPlot.comet.Rd coMET/man/printPlot.comet.nopval.Rd coMET/man/printPlot.comet.web.Rd coMET/man/psiQTL_GTEx.Rd coMET/man/read.config.Rd coMET/man/read.file.cormatrix.Rd coMET/man/read.file.mydata.Rd coMET/man/read.file.mydata.large.Rd coMET/man/refGenes_UCSC.Rd coMET/man/regulationBiomart_ENSEMBL.Rd coMET/man/regulatoryEvidenceBiomart_ENSEMBL.Rd coMET/man/regulatoryFeaturesBiomart_ENSEMBL.Rd coMET/man/regulatorySegmentsBiomart_ENSEMBL.Rd coMET/man/repeatMasker_UCSC.Rd coMET/man/retrieve.data.Rd coMET/man/segmentalDups_UCSC.Rd coMET/man/set.image.parameters.Rd coMET/man/snpBiomart_ENSEMBL.Rd coMET/man/snpLocations_UCSC.Rd coMET/man/structureBiomart_ENSEMBL.Rd coMET/man/transcript_ENSEMBL.Rd coMET/man/xenorefGenes_UCSC.Rd
coMET/tests
coMET/tests/runTests.R
coMET/vignettes
coMET/vignettes/biblio.bib
coMET/vignettes/coMET.Rnw
coMET/www
coMET/www/Readme.md
coMET/www/comet
coMET/www/comet/DESCRIPTION
coMET/www/comet/server.R
coMET/www/comet/ui.R
coMET/www/cometpdf
coMET/www/cometpdf/DESCRIPTION
coMET/www/cometpdf/server.R
coMET/www/cometpdf/ui.R
coMET/www/conf
coMET/www/conf/shiny-server.conf
coMET/www/config_cyp1b1_zoom.txt
coMET/www/config_cyp1b1_zoom_4webserver.txt
coMET/www/cyp1b1_infofile.txt
coMET/www/cyp1b1_infofile_exprGene_region.txt
coMET/www/cyp1b1_res37_rawMatrix.txt
coMET/www/cyp1b1_zoom_plus_name_expr.jpg
coMET/www/cyp1b1_zoom_plus_name_expr.pdf
coMET/www/cyp1b1info.txt
coMET/www/cyp1b1info_expr_reduce_region.txt
coMET/www/cyp1b1res_37.txt
coMET/www/minimal-cometwebPlot.jpeg

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.