Man pages for TiphaineCMartin/coMET_original
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

bindingMotifsBiomart_ENSEMBLCreates a binding motif track from ENSEMBL
check.configVarCheck if all variables have a value related to the functions...
check.configVar.cometlistCheck if all variables have a value related to the function...
check.format.mydataCheck the format of different data
ChIPTF_ENCODECreates a TF motif track from ENCODE
chromatinHMMAllCreating multiple chromHMM tracks from the UCSC genome...
chromatinHMMAll_UCSCCreating multiple chromHMM tracks from the UCSC genome...
chromatinHMMOne_UCSCCreating one chromHMM track from the UCSC genome browser
chromatinHMMRoadMapCreates a ChromHMM track from a file of RoadMap
chromHMM_RoadMapCreates a ChromHMM track from a file of RoadMap
chrUCSC2ENSEMBLRemoving "chr" to the chromosome number from UCSC to...
ClinVarCnvTrackCreate one track of the genomic positions of variants from...
ClinVarCnv_UCSCCreate one track of the genomic positions of variants from...
ClinVarMain_UCSCCreate one track of the genomic positions of variants from...
cometVisualize EWAS results in a genomic region of interest
comet.listList the correlations between omic features
coMET-packagevisualisation of regional epigenome-wide association scan...
comet.webVisualize EWAS results in a genomic region of interest with...
compute.cormatrixCompute the correlation matrix between CpG sites
CoreillCNVTrackCreate one track of the genomic positions of CNV in...
CoreillCNV_UCSCCreate one track of the genomic positions of CNV in...
COSMICTrackCreate one track of the genomic positions of variants from...
COSMIC_UCSCCreate one track of the genomic positions of variants from...
cpgIslands_UCSCcreate track CpG Island from UCSC
cpgPvalueCreate a plot of pvalue of CpG with DataTrack of Gviz
create.color.barCreate color bar of heatmap
create.color.listCreate color list for the main data
create.color.list.largeCreate list of colors for the supplementary data
createList.trackUserCreate list of Gviz's tracks from user's data
create.symbol.listcreate symbol list for the upper plot in the grid
create.symbol.list.largeCreate a list of symblo for the supplementary data
create.tracks.userCreate track from the user data
create.tracks.webCreate tracks for the web page (see cometweb)
datasetsData sets
dgfootprints_RoadMapCreates a track of DNA motif positional bias in digital...
DNaseI_FANTOMCreates a enhancer/promoter track from FANTOM
DNaseI_RoadMapCreates a promoter/enhancer regions track from a file of...
DNAse_UCSCCreation of an UCSC's DNase clusters track
draw.legendDisplay the legend of the plot
draw.name.genes.webdisplay the gene names
draw.name.tracks.webDisplay names of tracks for web page(see cometweb)
draw.plot.annotationDisplay the annotation track from ENSEMBL and UCSC
draw.plot.axis.dataDisplay the axis data of plot of pvalue
draw.plot.cometDisplay the three plots of coMET
draw.plot.comet.nopvalDisplay the three plots of coMET
draw.plot.comet.webDisplay the three plots of coMET for the web version
draw.plot.cormatrix.plotDisplay the correlation plot at the bottom of the grid
draw.plot.grid.mydataDisplay a plot of pvalue of data from MYDATA.FILE
draw.plot.grid.mydata.largeDisplay the plot of pvalue of the supplementary data
draw.plot.grid.mydata.namesDisplay the name of elements defined in DATA.FILE
draw.plot.grid.setupSet up the grid of plot
draw.plot.linesconnectionDisplay the connector lines for the probes
draw.plot.mydata.ggbioplot tracks created by ggbio that you want to visualise
eQTLCreates a track from a file for eQTL data
eQTL_GTExCreates a eQTL track from GTEx
fix.valuesFix and update the values of variables related to main data
fix.values.genericFix and update the values of generic variables
fix.values.largeFix and update the values of supplementary data
GAD_UCSCCreate one track of the genomic positions of variants from...
gcContent_UCSCCreate one track of GC content from UCSC
GeneReviews_UCSCCreate one track of the genomic positions of variants from...
genes_ENSEMBLCreate one track of the genes in the genomic regions of...
genesName_ENSEMBLObtain the genes names in the genomic regions of interest...
GWAScatalog_UCSCCreate one track of the genomic positions of variants from...
HiCdata2matrixCreates a HiC matrix from a file (Rao et al., 2014)
HistoneAll_UCSCCreate multiple tracks of histone modifications from the UCSC...
HistoneOne_UCSCCreate one track of one histone modification profile from the...
imprintedGenes_GTExCreates a imprinted genes track from GTEx
interestGenes_ENSEMBLCreate one track of the genes in the genomic regions of...
interestTranscript_ENSEMBLCreate a track of transcripts from ENSEMBL
ISCA_UCSCCreate one track of the genomic positions of variants from...
knownGenesUCSCCreate a track of known genes from the UCSC genome browser
knownGenes_UCSCCreate a track of known genes from the UCSC genome browser
metQTLCreates a track from a file for metQTL data
miRNATargetRegionsBiomartCreates a track of miRNA target regions from ENSEMBL
miRNATargetRegionsBiomart_ENSEMBLCreates a track of miRNA target regions from ENSEMBL
OtherRegulatoryRegionsBiomartCreates a track of other regulatory regions from ENSEMBL
otherRegulatoryRegionsBiomart_ENSEMBLCreates a track of other regulatory regions from ENSEMBL
printPlot.cometCreate the plot on file from coMet function
printPlot.comet.nopvalCreate the plot on file from coMet function
printPlot.comet.webDisplay the plot from cometWeb funciton
psiQTL_GTExCreates a psiQTL track from GTEx
read.configExtract the values of variables from configuration file
read.file.cormatrixRead, compute and extract the values from correlation matrix...
read.file.mydataRead the files of main data and extract data
read.file.mydata.largeRead the files of supplemantary data and extract data
refGenes_UCSCCreate a track of RefSeq genes from the UCSC genome browser
regulationBiomart_ENSEMBLCreate a regulation track from ENSEMBL
regulatoryEvidenceBiomart_ENSEMBLCreates a regulatory feature track from ENSEMBL
RegulatoryFeaturesBiomart Creates a regulatory feature track from ENSEMBL
regulatoryFeaturesBiomart_ENSEMBLCreates a regulatory feature track from ENSEMBL
RegulatorySegmentsBiomartCreates a binding motif track from ENSEMBL
regulatorySegmentsBiomart_ENSEMBLCreates a binding motif track from ENSEMBL
repeatMasker_UCSCCreate one track of the genomic positions of regions from...
retrieve.dataRetrieve the data from configuration file and data files
segmentalDups_UCSCCreate one track of the genomic positions of regions from...
SegmentalDupsUCSCCreate one track of the genomic positions of regions from...
set.image.parametersSet up the parameters of image
snpBiomart_ENSEMBLCreate a short variation track from ENSEMBL
snpLocations_UCSCCreate a SNP track from UCSC
structureBiomart_ENSEMBLCreate a structural variation track from ENSEMBL
TFBS_FANTOMCreates a TFBS motif track from FANTOM
transcript_ENSEMBLCreate a track of transcripts from ENSEMBL
xenorefGenes_UCSCCreate a track for xeno-reference genes from the UCSC genome...
TiphaineCMartin/coMET_original documentation built on May 10, 2017, 4:53 p.m.