Man pages for TiphaineCMartin/coMET_original
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
| 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 | Creating multiple chromHMM tracks from the UCSC genome... |
| chromatinHMMAll_UCSC | Creating multiple chromHMM tracks from the UCSC genome... |
| chromatinHMMOne_UCSC | Creating one chromHMM track from the UCSC genome browser |
| chromatinHMMRoadMap | Creates a ChromHMM track from a file of RoadMap |
| chromHMM_RoadMap | Creates a ChromHMM track from a file of RoadMap |
| chrUCSC2ENSEMBL | Removing "chr" to the chromosome number from UCSC to... |
| ClinVarCnvTrack | Create one track of the genomic positions of variants from... |
| 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 |
| CoreillCNVTrack | Create one track of the genomic positions of CNV in... |
| CoreillCNV_UCSC | Create one track of the genomic positions of CNV in... |
| COSMICTrack | Create one track of the genomic positions of variants from... |
| 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... |
| knownGenesUCSC | Create a track of known genes from the UCSC genome browser |
| knownGenes_UCSC | Create a track of known genes from the UCSC genome browser |
| metQTL | Creates a track from a file for metQTL data |
| miRNATargetRegionsBiomart | Creates a track of miRNA target regions from ENSEMBL |
| miRNATargetRegionsBiomart_ENSEMBL | Creates a track of miRNA target regions from ENSEMBL |
| OtherRegulatoryRegionsBiomart | Creates a track of other regulatory 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 | Creates a regulatory feature track from ENSEMBL |
| regulatoryFeaturesBiomart_ENSEMBL | Creates a regulatory feature track from ENSEMBL |
| RegulatorySegmentsBiomart | Creates a binding motif 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... |
| SegmentalDupsUCSC | 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... |
