coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
Version 1.8.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorTiphaine C. Martin, Thomas Hardiman, Idil Yet, Pei-Chien Tsai, Jordana T. Bell
Bioconductor views ChIPSeq DNAMethylation DNASeq DifferentialMethylation ExomeSeq FunctionalGenomics Genetics GenomeWideAssociation MethylSeq MethylationArray Microarray RNASeq RiboSeq Sequencing Software Visualization
Date of publicationNone
MaintainerTiphaine Martin <tiphaine.martin@kcl.ac.uk>
LicenseGPL (>= 2)
Version1.8.0
URL http://epigen.kcl.ac.uk/comet
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("coMET")

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...

Functions

BindingMotifAll Man page
BindingMotifMultiple Man page
BindingMotifSingle Man page
COSMIC_UCSC Man page Source code
ChIPTF_ENCODE Man page Source code
ClinVarCnv_UCSC Man page Source code
ClinVarMain_UCSC Man page Source code
CoreillCNV_UCSC Man page Source code
DNAse_UCSC Man page Source code
DNaseI_FANTOM Man page Source code
DNaseI_RoadMap Man page Source code
DNaseI_RoadMapSingle Man page
DupTrack Man page
GAD_UCSC Man page Source code
GWAScatalog_UCSC Man page Source code
GeneReviews_UCSC Man page Source code
HiCdata2matrix Man page Source code
HistoneAll_UCSC Man page Source code
HistoneOne_UCSC Man page Source code
ISCA_UCSC Man page Source code
OtherRegulatoryRegionsTrackAll Man page
OtherRegulatoryRegionsTrackSingle Man page
PancreasIG Man page
PancreasIGtrack Man page
PancreasimprintedIG Man page
PancreasimprintedIGtrack Man page
RegulatoryEvidenceBiomartTrackAll Man page
RegulatoryEvidenceBiomartTrackMultiple Man page
RegulatoryEvidenceBiomartTrackSingle Man page
RegulatoryFeaturesBiomartTrackAll Man page
RegulatoryFeaturesBiomartTrackMultiple Man page
RegulatoryFeaturesBiomartTrackSingle Man page
RegulatorySegmentsBiomartTrackAll Man page
RegulatorySegmentsBiomartTrackMultiple Man page
RegulatorySegmentsBiomartTrackSingle Man page
StomachIG Man page
StomachIGtrack Man page
TFBS_FANTOM Man page Source code
allIG Man page
allIGtrack Man page
allimprintedIG Man page
allimprintedIGtrack Man page
bindMotifsBiomartTrackAll Man page
bindMotifsBiomartTrackDouble Man page
bindMotifsBiomartTrackMultiple Man page
bindMotifsBiomartTrackSingle Man page
bindingMotifsBiomart_ENSEMBL Man page Source code
check.configVar Man page Source code
check.configVar.cometlist Source code
check.configVarcometlist Man page
check.format.mydata Man page Source code
chipTFtrack Man page
chrUCSC2ENSEMBL Man page Source code
chromHMM_RoadMap Man page Source code
chromHMM_RoadMapAll Man page
chromHMM_RoadMapAllE063 Man page
chromHMM_RoadMapMultiple Man page
chromHMM_RoadMapSingle Man page
chromatinHMMAll_UCSC Man page Source code
chromatinHMMOne_UCSC Man page Source code
chromatinHMMRoadMapAll Man page
chromatinHMMRoadMapMultiple Man page
chromatinHMMRoadMapSingle Man page
chromhmmNoPattern Man page
chromhmmPattern Man page
chromhmmtrackone Man page
clinCNV Man page
clinVariant Man page
coMET Man page
coMET-package Man page
comet Man page Source code
comet.list Man page Source code
comet.web Man page Source code
compute.cormatrix Man page Source code
coreilVariant Man page
cosmicVariant Man page
cpgIslands_UCSC Man page Source code
cpgIslandtrack Man page
cpgIstrack Man page
cpgPvalue Man page Source code
create.color.bar Man page Source code
create.color.list Man page Source code
create.color.list.large Man page Source code
create.symbol.list Man page Source code
create.symbol.list.large Man page Source code
create.tracks.user Man page Source code
create.tracks.web Man page Source code
createList.trackUser Man page Source code
dgfootprints_RoadMap Man page Source code
dgfootprints_RoadMapSingle Man page
dnasetrack Man page
draw.legend Man page Source code
draw.name.genes.web Man page Source code
draw.name.tracks.web Man page Source code
draw.plot.annotation Man page Source code
draw.plot.axis.data Man page Source code
draw.plot.comet Man page Source code
draw.plot.comet.nopval Man page Source code
draw.plot.comet.web Man page Source code
draw.plot.cormatrix.plot Man page Source code
draw.plot.grid.mydata Man page Source code
draw.plot.grid.mydata.large Man page Source code
draw.plot.grid.mydata.names Man page Source code
draw.plot.grid.setup Man page Source code
draw.plot.linesconnection Man page Source code
draw.plot.mydata.ggbio Man page Source code
dyaRM Man page
dyaRMtrack Man page
eGTexTrackSNP Man page
eGTexTrackall Man page
eQTL Man page Source code
eQTLTrackAll Man page
eQTLTrackMultiple Man page
eQTLTrackSingle Man page
eQTL_GTEx Man page Source code
enhFANTOMtrack Man page
enhRM Man page
enhRMtrack Man page
fix.values Man page Source code
fix.values.generic Man page Source code
fix.values.large Man page Source code
gadtrack Man page
gcContent_UCSC Man page Source code
gctrack Man page
geneExpression_GTEx Source code
geneNameEnsembl Man page
geneRtrack Man page
genesName_ENSEMBL Man page Source code
genesUcsctrack Man page
genes_ENSEMBL Man page Source code
genetrack Man page
grtrack Man page
grtrack4eGTex Man page
gwastrack Man page
histonalltrack Man page
histoneonetrack Man page
imprintedGenesGTEx Man page
imprintedGenes_GTEx Man page Source code
interestGenes_ENSEMBL Man page Source code
interestTranscript_ENSEMBL Man page Source code
interestgenesENSMBLtrack Man page
interesttransENSMBLtrack Man page
iscatrack Man page
knownGenes_UCSC Man page Source code
matrix_HiC_Rao Man page
metQTL Man page Source code
metQTLTrackAll Man page
metQTLTrackMultiple Man page
metQTLTrackSingle Man page
miRNATargetRegionsBiomartTrack Man page
miRNATargetRegionsBiomart_ENSEMBL Man page Source code
otherRegulatoryRegionsTrackAll Man page
otherRegulatoryRegionsTrackSingle Man page
otherRegulatoryRegions_ENSEMBL Man page Source code
printPlot.comet Man page Source code
printPlot.comet.nopval Man page Source code
printPlot.comet.web Man page Source code
promRMtrack Man page
promRMtrackE063 Man page
psiGTex Man page
psiGTexTrackSNP Man page
psiGTexTrackall Man page
psiQTL_GTEx Man page Source code
read.config Man page Source code
read.file.cormatrix Man page Source code
read.file.mydata Man page Source code
read.file.mydata.large Man page Source code
refGenes_UCSC Man page Source code
regulationBiomart_ENSEMBL Man page Source code
regulationENSEMBLtrack Man page
regulatoryEvidenceBiomartTrackAll Man page
regulatoryEvidenceBiomartTrackMultiple Man page
regulatoryEvidenceBiomartTrackSingle Man page
regulatoryEvidenceBiomart_ENSEMBL Man page Source code
regulatoryFeaturesBiomartTrackAll Man page
regulatoryFeaturesBiomartTrackMultiple Man page
regulatoryFeaturesBiomartTrackSingle Man page
regulatoryFeaturesBiomart_ENSEMBL Man page Source code
regulatorySegmentsBiomartTrackAll Man page
regulatorySegmentsBiomartTrackMultiple Man page
regulatorySegmentsBiomartTrackSingle Man page
regulatorySegmentsBiomart_ENSEMBL Man page Source code
repeatMaskerTrack Man page
repeatMasker_UCSC Man page Source code
retrieve.data Man page Source code
retrieve.data.cometlist Source code
rmtrack Man page
segmentalDups_UCSC Man page Source code
set.image.parameters Man page Source code
snpBiomart_ENSEMBL Man page Source code
snpLocations_UCSC Man page Source code
snpUCSCtrack Man page
snptrack Man page
structureBiomart_ENSEMBL Man page Source code
strutrack Man page
tfbsFANTOMtrack Man page
transENSMBLtrack Man page
transcript_ENSEMBL Man page Source code
write.comet.list Source code
xenogenestrack Man page
xenorefGenes_UCSC Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/AnalyseFile.R
R/BiofeatureGraphics.R
R/DrawPlot.R
R/GeneralMethodComet.R
R/comet.R
R/cometWeb.R
R/cometlist.R
README.md
build
build/vignette.rds
data
data/BindingMotifAll.rda
data/BindingMotifMultiple.rda
data/BindingMotifSingle.rda
data/ClinVarCnvTrack.rda
data/CoreillCNVTrack.rda
data/DNaseI_RoadMapSingle.rda
data/DupTrack.rda
data/GWASTrack.rda
data/GeneReviewTrack.rda
data/GeneReviewsTrack.rda
data/ISCAtrack.rda
data/ISCAtrack_Grch38.rda
data/OtherRegulatoryRegionsAll.rda
data/OtherRegulatoryRegionsSingle.rda
data/PancreasIG.rda
data/PancreasIGtrack.rda
data/PancreasimprintedIG.rda
data/PancreasimprintedIGtrack.rda
data/RegulatoryEvidenceBiomartAll.rda
data/RegulatoryEvidenceBiomartMultiple.rda
data/RegulatoryEvidenceBiomartSingle.rda
data/RegulatoryFeaturesBiomartAll.rda
data/RegulatoryFeaturesBiomartMultiple.rda
data/RegulatoryFeaturesBiomartSingle.rda
data/RegulatorySegmentsBiomartAll.rda
data/RegulatorySegmentsBiomartMultiple.rda
data/RegulatorySegmentsBiomartSingle.rda
data/SegmentalDupsUCSC.rda
data/StomachIG.rda
data/StomachIGtrack.rda
data/allIG.rda
data/allIGtrack.rda
data/allimprintedIG.rda
data/allimprintedIGtrack.rda
data/bindMotifsBiomartTrackAll.rda
data/bindMotifsBiomartTrackMultiple.rda
data/bindMotifsBiomartTrackSingle.rda
data/bindingMotifsBiomartAll.rda
data/bindingMotifsBiomartMultiple.rda
data/bindingMotifsBiomartSingle.rda
data/chipTFtrack.rda
data/chipTFtrack_old.rda
data/chromHMM_RoadMapAll.rda
data/chromHMM_RoadMapAllE063.rda
data/chromHMM_RoadMapMultiple.rda
data/chromHMM_RoadMapSingle.rda
data/chromatinHMMRoadMapAll.rda
data/chromatinHMMRoadMapMultiple.rda
data/chromatinHMMRoadMapSingle.rda
data/chromhmmNoPattern.rda
data/chromhmmPattern.rda
data/chromhmmtrackone.rda
data/clinVarMaintrack.rda
data/coreilVarianttrack.rda
data/cosmicVarianttrack.rda
data/cpgIslandsUCSC.rda
data/cpgIslandtrack.rda
data/datalist
data/dgfootprints_RoadMapSingle.rda
data/dnasetrack.rda
data/dyaRM.rda
data/dyaRMtrack.rda
data/eGTexTrackSNP.rda
data/eGTexTrackall.rda
data/eQTLAll.rda
data/eQTLMultiple.rda
data/eQTLSingle.rda
data/eQTLTrackAll.rda
data/eQTLTrackMultiple.rda
data/eQTLTrackSingle.rda
data/enhFANTOMtrack.rda
data/enhRM.rda
data/enhRMtrack.rda
data/gadtrack.rda
data/gcContent.rda
data/gctrack.rda
data/geneENSEMBLtrack.rda
data/geneNameEnsembl.rda
data/genesENSEMBL.rda
data/genesGencodetrack.rda
data/genesNameENSEMBL.rda
data/genesUcsctrack.rda
data/genetrack4RM.rda
data/genetrack4psiGTEX.rda
data/grtrack4eGTex.rda
data/histonalltrack.rda
data/histoneonetrack.rda
data/imprintedGenesGTEx.rda
data/interestGenesENSEMBL.rda
data/interestTranscriptENSEMBL.rda
data/interestgenesENSMBLtrack.rda
data/interesttransENSMBLtrack.rda
data/knownGenesUCSC.rda
data/matrix_HiC_Rao.rda
data/metQTLSingle.rda
data/metQTLTrackAll.rda
data/metQTLTrackMultiple.rda
data/metQTLTrackSingle.rda
data/miRNATargetRegionsBiomart.rda
data/miRNATargetRegionsBiomartTrack.rda
data/otherRegulatoryRegionsTrackAll.rda
data/otherRegulatoryRegionsTrackSingle.rda
data/promRMtrack.rda
data/promRMtrackE063.rda
data/psiGTex.rda
data/psiGTexTrackSNP.rda
data/psiGTexTrackall.rda
data/refGenesUCSC.rda
data/regulationENSEMBLtrack.rda
data/regulatoryEvidenceBiomartTrackAll.rda
data/regulatoryEvidenceBiomartTrackMultiple.rda
data/regulatoryEvidenceBiomartTrackSingle.rda
data/regulatoryFeaturesBiomartTrackAll.rda
data/regulatoryFeaturesBiomartTrackMultiple.rda
data/regulatoryFeaturesBiomartTrackSingle.rda
data/regulatorySegmentsBiomartTrackAll.rda
data/regulatorySegmentsBiomartTrackMultiple.rda
data/regulatorySegmentsBiomartTrackSingle.rda
data/repeatMaskerTrack.rda
data/snpBiomart.rda
data/snpBiomarttrack.rda
data/snpUCSCtrack.rda
data/snptrack.rda
data/strucBiomarttrack.rda
data/structureBiomart.rda
data/tfbsFANTOMtrack.rda
data/transENSMBLtrack.rda
data/xenogenestrack.rda
data/xenorefGenesUCSC.rda
inst
inst/CITATION
inst/doc
inst/doc/coMET.R
inst/doc/coMET.Rnw
inst/doc/coMET.pdf
inst/extdata
inst/extdata/JpegTables
inst/extdata/JpegTables/BindingMotifsBiomart.jpg
inst/extdata/JpegTables/ChromHMM.jpg
inst/extdata/JpegTables/ChromHMM_UCSC.jpg
inst/extdata/JpegTables/ChromHMM_coMET.jpg
inst/extdata/JpegTables/ISCATrack.jpg
inst/extdata/JpegTables/ISCATrack_old.jpg
inst/extdata/JpegTables/OtherRegulatoryRegions.jpg
inst/extdata/JpegTables/RegulatoryElementsENSEMBL.jpg
inst/extdata/JpegTables/RegulatoryEvidence_1.jpg
inst/extdata/JpegTables/RegulatoryEvidence_2.jpg
inst/extdata/JpegTables/RegulatoryEvidence_3.jpg
inst/extdata/JpegTables/RegulatoryFeaturesBiomart.jpg
inst/extdata/JpegTables/RegulatorySegmentsBiomart.jpg
inst/extdata/JpegTables/RoadMap15_RoadMap.jpg
inst/extdata/JpegTables/RoadMap18_RoadMap.jpg
inst/extdata/JpegTables/RoadMap18_coMET.jpg
inst/extdata/JpegTables/RoadMap25_RoadMap.jpg
inst/extdata/JpegTables/RoadMap25_coMET.jpg
inst/extdata/JpegTables/bindingMotifBiomart.jpg
inst/extdata/JpegTables/eQTL.jpg
inst/extdata/JpegTables/metQTL.jpg
inst/extdata/JpegTables/structureBiomart.jpg
inst/extdata/config_cyp1b1_zoom.txt
inst/extdata/config_cyp1b1_zoom_4comet.txt
inst/extdata/config_cyp1b1_zoom_4cometnopval.txt
inst/extdata/config_cyp1b1_zoom_4cometnopval_Grch38.txt
inst/extdata/config_cyp1b1_zoom_4nomatrix.txt
inst/extdata/config_cyp1b1_zoom_4nomatrix_Grch38.txt
inst/extdata/config_cyp1b1_zoom_4webserver.txt
inst/extdata/config_cyp1b1_zoom_4webserver_Grch38.txt
inst/extdata/config_gata55_larger_article.txt
inst/extdata/config_gata55_larger_article_rev.txt
inst/extdata/cyp1b1_infofile.bed
inst/extdata/cyp1b1_infofile.txt
inst/extdata/cyp1b1_infofile_Grch38.txt
inst/extdata/cyp1b1_infofile_bed.txt
inst/extdata/cyp1b1_infofile_bed_v2.bed
inst/extdata/cyp1b1_infofile_bed_v2.txt
inst/extdata/cyp1b1_infofile_bed_v2_hg38.bed
inst/extdata/cyp1b1_infofile_bed_v3.bed
inst/extdata/cyp1b1_infofile_bed_v3.txt
inst/extdata/cyp1b1_infofile_bed_v3_hg38.bed
inst/extdata/cyp1b1_infofile_exprGene_region.txt
inst/extdata/cyp1b1_infofile_exprGene_region_Grch38.txt
inst/extdata/cyp1b1_infofile_exprGene_region_v2.csv
inst/extdata/cyp1b1_res37_cormatrix_list_BH05.txt
inst/extdata/cyp1b1_res37_rawMatrix.txt
inst/extdata/cyp1b1_zoom_plus_name_expr.pdf
inst/extdata/datalist
inst/extdata/gata4_55probes_info.txt
inst/extdata/gata4_55probes_rawMatrix.txt
inst/extdata/gata4_55probes_residuals.txt
inst/extdata/gata4_95probes_info.txt
inst/extdata/gata_comet_55probes_large_article.eps
inst/extdata/gata_comet_55probes_large_article_gene.eps
inst/extdata/gata_comet_55probes_large_article_rev.eps
inst/unitTests
inst/unitTests/ChangeLog.txt
inst/unitTests/Citation.txt
inst/unitTests/test_chrUCSC2ENSEMBL.R
man
man/COSMIC_UCSC.Rd
man/ChIPTF_ENCODE.Rd
man/ClinVarCnv_UCSC.Rd
man/ClinVarMain_UCSC.Rd
man/CoreillCNV_UCSC.Rd
man/DNAse_UCSC.Rd
man/DNaseI_FANTOM.Rd
man/DNaseI_RoadMap.Rd
man/GAD_UCSC.Rd
man/GWAScatalog_UCSC.Rd
man/GeneReviews_UCSC.Rd
man/HiCdata2matrix.Rd
man/HistoneAll_UCSC.Rd
man/HistoneOne_UCSC.Rd
man/ISCA_UCSC.Rd
man/TFBS_FANTOM.Rd
man/bindingMotifsBiomart_ENSEMBL.Rd
man/check.configVar.Rd
man/check.configVar.cometlist.Rd
man/check.format.mydata.Rd
man/chrUCSC2ENSEMBL.Rd
man/chromHMM_RoadMap.Rd
man/chromatinHMMAll_UCSC.Rd
man/chromatinHMMOne_UCSC.Rd
man/coMET-package.Rd
man/comet.Rd
man/comet.list.Rd
man/comet.web.Rd
man/compute.cormatrix.Rd
man/cpgIslands_UCSC.Rd
man/cpgPvalue.Rd
man/create.color.bar.Rd
man/create.color.list.Rd
man/create.color.list.large.Rd
man/create.symbol.list.Rd
man/create.symbol.list.large.Rd
man/create.tracks.user.Rd
man/create.tracks.web.Rd
man/createList.trackUser.Rd
man/datasets.Rd
man/dgfootprints_RoadMap.Rd
man/draw.legend.Rd
man/draw.name.genes.web.Rd
man/draw.name.tracks.web.Rd
man/draw.plot.annotation.Rd
man/draw.plot.axis.data.Rd
man/draw.plot.comet.Rd
man/draw.plot.comet.nopval.Rd
man/draw.plot.comet.web.Rd
man/draw.plot.cormatrix.plot.Rd
man/draw.plot.grid.mydata.Rd
man/draw.plot.grid.mydata.large.Rd
man/draw.plot.grid.mydata.names.Rd
man/draw.plot.grid.setup.Rd
man/draw.plot.linesconnection.Rd
man/draw.plot.mydata.ggbio.Rd
man/eQTL.Rd
man/eQTL_GTEx.Rd
man/fix.values.Rd
man/fix.values.generic.Rd
man/fix.values.large.Rd
man/gcContent_UCSC.Rd
man/genesName_ENSEMBL.Rd
man/genes_ENSEMBL.Rd
man/imprintedGenes_GTEx.Rd
man/interestGenes_ENSEMBL.Rd
man/interestTranscript_ENSEMBL.Rd
man/knownGenes_UCSC.Rd
man/metQTL.Rd
man/miRNATargetRegionsBiomart_ENSEMBL.Rd
man/otherRegulatoryRegionsBiomart_ENSEMBL.Rd
man/printPlot.comet.Rd
man/printPlot.comet.nopval.Rd
man/printPlot.comet.web.Rd
man/psiQTL_GTEx.Rd
man/read.config.Rd
man/read.file.cormatrix.Rd
man/read.file.mydata.Rd
man/read.file.mydata.large.Rd
man/refGenes_UCSC.Rd
man/regulationBiomart_ENSEMBL.Rd
man/regulatoryEvidenceBiomart_ENSEMBL.Rd
man/regulatoryFeaturesBiomart_ENSEMBL.Rd
man/regulatorySegmentsBiomart_ENSEMBL.Rd
man/repeatMasker_UCSC.Rd
man/retrieve.data.Rd
man/segmentalDups_UCSC.Rd
man/set.image.parameters.Rd
man/snpBiomart_ENSEMBL.Rd
man/snpLocations_UCSC.Rd
man/structureBiomart_ENSEMBL.Rd
man/transcript_ENSEMBL.Rd
man/xenorefGenes_UCSC.Rd
tests
tests/runTests.R
vignettes
vignettes/biblio.bib
vignettes/coMET.Rnw
www
www/Readme.md
www/comet
www/comet/DESCRIPTION
www/comet/server.R
www/comet/ui.R
www/cometpdf
www/cometpdf/DESCRIPTION
www/cometpdf/server.R
www/cometpdf/ui.R
www/conf
www/conf/shiny-server.conf
www/config_cyp1b1_zoom.txt
www/config_cyp1b1_zoom_4webserver.txt
www/cyp1b1_infofile.txt
www/cyp1b1_infofile_exprGene_region.txt
www/cyp1b1_res37_rawMatrix.txt
www/cyp1b1_zoom_plus_name_expr.jpg
www/cyp1b1_zoom_plus_name_expr.pdf
www/cyp1b1info.txt
www/cyp1b1info_expr_reduce_region.txt
www/cyp1b1res_37.txt
www/minimal-cometwebPlot.jpeg
coMET documentation built on May 20, 2017, 10:31 p.m.