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

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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.

Author
Tiphaine C. Martin, Thomas Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T. Bell
Date of publication
None
Maintainer
Tiphaine Martin <tiphaine.martin@kcl.ac.uk>
License
GPL (>= 2)
Version
1.6.0
URLs

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