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coMET

##Overview The coMET package is a web-based plotting tool and R-based package to visualize different genome-wide association scans such as EWAS (epigenome-wide association scan) results in a genomic region of interest. coMET provides a plot of the EWAS association signal and visualisation of the methylation correlation between CpG sites (co-methylation). The coMET package also provides the option to annotate the region using functional genomic information, including both user-defined features and pre-selected features based on the Encode project. The plot can be customized with different parameters, such as plot labels, colours, symbols, heatmap colour scheme, significance thresholds, and including reference CpG sites. Finally, the tool can also be applied to display the correlation patterns of other genomic data and any species, e.g. gene expression array data.

##coMET webservice

The webservice is the pre-formated web service of coMET with a reduction of parameters availlable.

Go to : http://www.epigen.kcl.ac.uk/comet or directly one of instance: http://comet.epigen.kcl.ac.uk:3838/coMET/

##Developpers

coMET is developed by Tiphaine C. Martin in collaboration with Idil Erte, Pei-Chien Tsai, Jordana T.Bell, Department of Twin Research, Kings College London.

##Cite

Martin, T.C, Erte, I, Tsai, P-C, Bell, J.T.,coMET: an R plotting package to visualize regional plots of epigenome-wide association scan results, QC14, 2014.

##Contacts

For any question, you can send an email to Tiphaine Martin (tiphaine.martin at kcl.ac.uk) and Jordana Bell (jordana.bell at kcl.ac.uk)

##More information

Go to the website Department of Twin Research :http://epigen.kcl.ac.uk/comet

Go to the help of coMET webservice : http://comet.epigen.kcl.ac.uk:3838/coMET/

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Version

Version

1.4.4

License

GPL (>= 2)

Maintainer

Tiphaine Martin

Last Published

February 15th, 2017

Functions in coMET (1.4.4)

chromHMM_RoadMap

Creates a ChromHMM track from a file of RoadMap

create.symbol.list.large

Create a list of symblo for the supplementary data

create.symbol.list

create symbol list for the upper plot in the grid

Creates a track from a file for eQTL data

Create one track of GC content from UCSC

fix.values.generic

Fix and update the values of generic variables

Create one track of the genomic positions of variants from the Genetic Association Database (GAD)

chromatinHMMOne_UCSC

Creating one chromHMM track from the UCSC genome browser

compute.cormatrix

Compute the correlation matrix between CpG sites

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

miRNATargetRegionsBiomart_ENSEMBL

Creates a track of miRNA target regions from ENSEMBL

Creates a track from a file for metQTL data

read.file.cormatrix

Read, compute and extract the values from correlation matrix file

read.file.mydata

Read the files of main data and extract data

snpLocations_UCSC

Create a SNP track from UCSC

snpBiomart_ENSEMBL

Create a short variation track from ENSEMBL

chromatinHMMAll_UCSC

Creating multiple chromHMM tracks from the UCSC genome browser

Creates a TF motif track from ENCODE

ClinVarMain_UCSC

Create one track of the genomic positions of variants from the ClinVar database (variants only)

visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns (and also for other omic-WAS)

Creates a enhancer/promoter track from FANTOM

Creates a promoter/enhancer regions track from a file of RoadMap

Fix and update the values of variables related to main data

Create one track of the genomic positions of variants from ISCA (obselete database)

fix.values.large

Fix and update the values of supplementary data

knownGenes_UCSC

Create a track of known genes from the UCSC genome browser

Creates a psiQTL track from GTEx

Extract the values of variables from configuration file

regulatoryFeaturesBiomart_ENSEMBL

Creates a regulatory feature track from ENSEMBL

regulatorySegmentsBiomart_ENSEMBL

Creates a binding motif track from ENSEMBL

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)

Create one track of the genomic positions of variants from COSMIC

cpgIslands_UCSC

create track CpG Island from UCSC

create.tracks.web

Create tracks for the web page (see cometweb)

create.tracks.user

Create track from the user data

draw.plot.axis.data

Display the axis data of plot of pvalue

draw.plot.comet

Display the three plots of coMET

draw.plot.grid.mydata

Display a plot of pvalue of data from MYDATA.FILE

draw.plot.cormatrix.plot

Display the correlation plot at the bottom of the grid

otherRegulatoryRegions_ENSEMBL

Creates a track of other regulatory regions from ENSEMBL

regulationBiomart_ENSEMBL

Create a regulation track from ENSEMBL

printPlot.comet

Create the plot on file from coMet function

regulatoryEvidenceBiomart_ENSEMBL

Creates a regulatory feature track from ENSEMBL

structureBiomart_ENSEMBL

Create a structural variation track from ENSEMBL

Creates a TFBS motif track from FANTOM

dgfootprints_RoadMap

Creates a track of DNA motif positional bias in digital genomic Footprinting Sites (DGFP) from a file of RoadMap

Creation of an UCSC's DNase clusters track

draw.plot.grid.setup

Set up the grid of plot

draw.plot.comet.web

Display the three plots of coMET for the web version

draw.plot.comet.nopval

Display the three plots of coMET

draw.plot.linesconnection

Display the connector lines for the probes

genesName_ENSEMBL

Obtain the genes names in the genomic regions of interest from ENSEMBL

GWAScatalog_UCSC

Create one track of the genomic positions of variants from the GWAS catalog

imprintedGenes_GTEx

Creates a imprinted genes track from GTEx

HistoneOne_UCSC

Create one track of one histone modification profile from the UCSC genome browser

printPlot.comet.nopval

Create the plot on file from coMet function

repeatMasker_UCSC

Create one track of the genomic positions of regions from repeatMasker_UCSC

printPlot.comet.web

Display the plot from cometWeb funciton

check.configVar

Check if all variables have a value related to the functions comet and comet.web

Retrieve the data from configuration file and data files

check.format.mydata

Check the format of different data

Create a plot of pvalue of CpG with DataTrack of Gviz

create.color.bar

Create color bar of heatmap

createList.trackUser

Create list of Gviz's tracks from user's data

Display the legend of the plot

draw.name.genes.web

display the gene names

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

HistoneAll_UCSC

Create multiple tracks of histone modifications from the UCSC genome browser

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

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

read.file.mydata.large

Read the files of supplemantary data and extract data

Create a track of RefSeq genes from the UCSC genome browser

set.image.parameters

Set up the parameters of image

segmentalDups_UCSC

Create one track of the genomic positions of regions from segmentalDups_UCSC

bindingMotifsBiomart_ENSEMBL

Creates a binding motif track from ENSEMBL

check.configVar.cometlist

Check if all variables have a value related to the function comet.list. Comet.list gives the list of correlation between omic features.

Visualize EWAS results in a genomic region of interest

create.color.list

Create color list for the main data

List the correlations between omic features

create.color.list.large

Create list of colors for the supplementary data

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.mydata.ggbio

plot tracks created by ggbio that you want to visualise

GeneReviews_UCSC

Create one track of the genomic positions of variants from GeneReviews

Creates a eQTL track from GTEx

Create one track of the genes in the genomic regions of interest from EMSEMBL

xenorefGenes_UCSC

Create a track for xeno-reference genes from the UCSC genome browser

transcript_ENSEMBL

Create a track of transcripts from ENSEMBL