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 <firstname.lastname@example.org>|
|License||GPL (>= 2)|
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...