## ----setup, include=FALSE-------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----load_packages_models_templates, warning=FALSE, message=FALSE---------- # load packages library(InterMineR) library(Gviz) # load FlyMine and HumanMine im.fly = initInterMine(listMines()["FlyMine"]) # load templates templates.fly = getTemplates(im.fly) # load data models # model.fly = getModel(im.fly) # temporarily removed ## ----gene_info, warning=FALSE, message=FALSE------------------------------- # Build new query to retrieve information for zen, eve, and r Drosophila genes # Get Gene types from FlyMine model # head(subset(model.fly, type == "Gene"), 3) # temporarily removed gene_info.list = as.list(1:3) for(i in 1:3){ gene = c("zen", "eve", "r")[i] # define new query queryGeneIds = newQuery() queryGeneIds # set name queryGeneIds$name = "Gene identifiers" # set columns queryGeneIds$select = c( "Gene.primaryIdentifier", "Gene.secondaryIdentifier", "Gene.symbol", "Gene.id", "Gene.chromosome.primaryIdentifier", "Gene.chromosomeLocation.start", "Gene.chromosomeLocation.end", "Gene.chromosomeLocation.strand" ) # set sort order queryGeneIds$orderBy = list( c(Gene.secondaryIdentifier = "ASC") ) # set constraints newConstraint1 = list( path = "Gene", op = "LOOKUP", value = gene, code = "A" ) queryGeneIds$where = list(newConstraint1) # run query and store results gene_info.list[[i]] = runQuery(im = im.fly, qry = queryGeneIds) } # concatenate to data.frame gene_info.list = do.call(rbind, gene_info.list) # print dimensions print(dim(gene_info.list)) ## ----gene_info_InterMineR, warning=FALSE, message=FALSE-------------------- # set constraints constraints = setConstraints( paths = "Gene" , operators = "LOOKUP", values = list(c("zen", "eve", "r")) ) # define new query queryGeneIds = setQuery( select = c( "Gene.primaryIdentifier", "Gene.secondaryIdentifier", "Gene.symbol", "Gene.id", "Gene.chromosome.primaryIdentifier", "Gene.chromosomeLocation.start", "Gene.chromosomeLocation.end", "Gene.chromosomeLocation.strand" ), where = constraints ) # run query and store results gene_info = runQuery(im = im.fly, qry = queryGeneIds) # print dimensions print(dim(gene_info)) ## ----comparison, message=FALSE, warning=FALSE------------------------------ # compare the results from both type of queries all(gene_info == gene_info.list) gene_info ## ----Define_Template_Queries_1, warning=FALSE, message=FALSE--------------- # Retrieve Template Queries: # Use Gene_ExonLocation2 template query to get the exons for the genes of interest queryExons = getTemplateQuery( im.fly, name = "Gene_ExonLocation2") # Use Gene_AdjacentGenes template query to get the adjacent genes queryGeneAdjacentGenes = getTemplateQuery( im = im.fly, name = "Gene_AdjacentGenesLocations" ) # Use Gene_OverlapppingGenes template query to get the overlapping genes queryGeneOverlapppingGenes = getTemplateQuery( im.fly, name = "Gene_OverlapppingGenes" ) ## ----run_Template_Queries_1, warning=FALSE, message=FALSE------------------ for(i in 1:3){ gene = c("zen", "eve", "r")[i] # 1. Gene_ExonLocation2 # set Gene.secondaryIdentifier value queryExons$where[[1]]$value = gene_info[which(gene_info$Gene.symbol == gene),2] # or alternatively use setConstraints function queryExons$where = setConstraints( modifyQueryConstraints = queryExons, m.index = 1, values = list(gene_info[which(gene_info$Gene.symbol == gene),2]) ) # run query and save results assign( x = paste0(gene,".Exons"), value = runQuery(im.fly, queryExons) ) # 2. Gene_AdjacentGenes # change the value of the third constraint of the Gene_AdjacentGenes query with the # Gene.secondaryIdentifier of the genes of interest queryGeneAdjacentGenes$where[[3]]$value = gene_info$Gene.secondaryIdentifier[i] # or alternatively use setConstraints function queryGeneAdjacentGenes$where = setConstraints( modifyQueryConstraints = queryGeneAdjacentGenes, m.index = 3, values = list(gene_info$Gene.secondaryIdentifier[i]) ) # assign the adjacent gene information to each gene of interest assign(x = paste0(gene_info$Gene.symbol[i], "_AdjacentGenes"), value = runQuery(im.fly, queryGeneAdjacentGenes)) if(is.null(get(paste0(gene_info$Gene.symbol[i], "_AdjacentGenes")))){ print(paste0(gene_info$Gene.symbol[i], " query returns no adjacent genes")) } # 3. Gene_OverlapppingGenes queryGeneOverlapppingGenes$where[[2]]$value = gene_info$Gene.secondaryIdentifier[i] # or alternatively use setConstraints function queryGeneOverlapppingGenes$where = setConstraints( modifyQueryConstraints = queryGeneOverlapppingGenes, m.index = 2, values = list(gene_info$Gene.secondaryIdentifier[i]) ) assign(x = paste0(gene_info$Gene.symbol[i], "_OverlappingGenes"), value = runQuery(im.fly, queryGeneOverlapppingGenes)) if(is.null(get(paste0(gene_info$Gene.symbol[i], "_OverlappingGenes")))){ print(paste0(gene_info$Gene.symbol[i], " query returns no overlapping genes")) } } ## ----head_overlapping_adjacent, warning=FALSE, message=FALSE--------------- # show adjacent genes head(zen_AdjacentGenes, 3) head(r_AdjacentGenes, 3) # show overlapping genes head(eve_OverlappingGenes, 3) head(r_OverlappingGenes, 3) ## ----ROIs, warning=FALSE, message=FALSE------------------------------------ # get genomic region of zen, eve, r and their respective # adjacent and/or overlapping genes. # Add 1000 bp on both sides of this region! # chromosome region of interest (ROI) containing zen and adjacent genes zen.ROI.start = min( as.numeric(zen_AdjacentGenes[,grep("start", colnames(zen_AdjacentGenes))]) ) - 1000 zen.ROI.end = max( as.numeric(zen_AdjacentGenes[,grep("end", colnames(zen_AdjacentGenes))]) ) + 1000 # chromosome region of interest (ROI) containing eve and overlapping genes eve.ROI.start = min( as.numeric(eve_OverlappingGenes[,grep("start", colnames(eve_OverlappingGenes))]) ) - 1000 eve.ROI.end = max( as.numeric(eve_OverlappingGenes[,grep("end", colnames(eve_OverlappingGenes))]) ) + 1000 # chromosome region of interest (ROI) containing r, adjacent and overlapping genes r.ROI.start = min( as.numeric( c(r_OverlappingGenes[,grep("start", colnames(r_OverlappingGenes))], r_AdjacentGenes[,grep("start", colnames(r_AdjacentGenes))]) ) ) - 1000 r.ROI.end = max( as.numeric( c(r_OverlappingGenes[,grep("end", colnames(r_OverlappingGenes))], r_AdjacentGenes[,grep("end", colnames(r_AdjacentGenes))]) ) ) + 1000 ## ----Define_Template_Queries_2, warning=FALSE, message=FALSE--------------- # find all transcription factor (TF) binding sites within the ROIs # by using the ChromLocation_TFBindingSiteLocationGeneFactor template query queryTFBindingSites = getTemplateQuery( im.fly, "ChromLocation_TFBindingSiteLocationGeneFactor" ) # find all Regulatory Regions (RRs) within the ROIs # by using the ChromLocation_RegulatoryRegion template query queryRRLocations = getTemplateQuery( im.fly, "ChromLocation_RegulatoryRegion" ) ## ----run_Template_Queries_2, warning=FALSE, message=FALSE------------------ for(i in 1:3){ gene = c("zen", "eve", "r")[i] # 1. ChromLocation_TFBindingSiteLocationGeneFactor # set chromosome value queryTFBindingSites$where[[3]]$value = gene_info[which(gene_info$Gene.symbol == gene),5] # set location start queryTFBindingSites$where[[4]]$value = as.character(get(paste0(gene,".ROI.start"))) # set location end queryTFBindingSites$where[[5]]$value = as.character(get(paste0(gene,".ROI.end"))) # or alternatively use setConstraints function queryTFBindingSites$where = setConstraints( modifyQueryConstraints = queryTFBindingSites, m.index = 3:5, values = list( # set chromosome value gene_info[which(gene_info$Gene.symbol == gene),5], # set location start as.character(get(paste0(gene,".ROI.start"))), # set location end as.character(get(paste0(gene,".ROI.end"))) ) ) # run query and save results assign( x = paste0(gene, ".ROI.TFBindingSites"), value = runQuery(im.fly, queryTFBindingSites) ) if(is.null(get(paste0(gene, ".ROI.TFBindingSites")))){ print(paste0(gene, " ROI query returns no TF binding sites from REDfly database")) } # 2. ChromLocation_RegulatoryRegion # set chromosome value queryRRLocations$where[[1]]$value = gene_info[which(gene_info$Gene.symbol == gene),5] # set location start queryRRLocations$where[[2]]$value = as.character(get(paste0(gene,".ROI.start"))) # set location end queryRRLocations$where[[3]]$value = as.character(get(paste0(gene,".ROI.end"))) # or alternatively use setConstraints function queryRRLocations$where = setConstraints( modifyQueryConstraints = queryRRLocations, m.index = 1:3, values = list( # set chromosome value gene_info[which(gene_info$Gene.symbol == gene),5], # set location start as.character(get(paste0(gene,".ROI.start"))), # set location end as.character(get(paste0(gene,".ROI.end"))) ) ) # run query and save results assign( x = paste0(gene, ".ROI.RRLocations"), value = runQuery(im.fly, queryRRLocations) ) if(is.null(get(paste0(gene, ".ROI.RRLocations")))){ print(paste0(gene, " ROI query returns no RRs")) } } ## ----head_TFBindingSites_RRs, warning=FALSE, message=FALSE----------------- head(zen.ROI.TFBindingSites, 3) head(eve.ROI.TFBindingSites, 3) head(r.ROI.TFBindingSites, 3) head(zen.ROI.RRLocations, 3) head(eve.ROI.RRLocations, 3) head(r.ROI.RRLocations, 3) ## ----UcscTrack, warning=FALSE, message=FALSE, eval=FALSE------------------- # for(i in 1:3){ # gene = c("zen", "eve", "r")[i] # # # set chromosome value # chrom = paste0("chr",gene_info[which(gene_info$Gene.symbol == gene),5]) # # # set the beginning and the end of the ROI # gene.start = get(paste0(gene, ".ROI.start")) # gene.end = get(paste0(gene, ".ROI.end")) # # # get CpG islands # assign( # x = paste0(gene, ".ROI.cpgIslands"), # value = UcscTrack(genome = "dm6", chromosome = chrom, # track = "cpgIslandExt", # from = gene.start, # to = gene.end, # trackType = "AnnotationTrack", # start = "chromStart", # end = "chromEnd", # id = "name", # shape = "box", # fill = "lightgreen", # name = "CpGs") # ) # # # get Conservation # assign( # x = paste0(gene, ".ROI.conservation"), # value = UcscTrack(genome = "dm6", chromosome = chrom, # track = "Conservation", # table = "phyloP27way", # from = gene.start, # to = gene.end, # trackType = "DataTrack", # start = "start", # end = "end", # data = "score", # type = "hist", # window = "auto", # col.histogram = "darkblue", # fill.histogram = "darkblue", # name = "Cons") # ) # # get GC Percent # assign( # x = paste0(gene, ".ROI.gcContent"), # value = UcscTrack(genome = "dm6", chromosome = chrom, # track = "GC Percent", # table = "gc5BaseBw", # from = gene.start, # to = gene.end, # trackType = "DataTrack", start = "start", # end = "end", data = "score", type = "hist", # window = "auto", # windowSize = 1500, fill.histogram = "#800080", # col.histogram = "#800080", # name = "GC%") # ) # } ## ----GenomeAxisTrack, warning=FALSE, message=FALSE, eval=FALSE------------- # # Plot all features for the genes of interest # axTrack <- GenomeAxisTrack() ## ----zen_vis, warning=FALSE, message=FALSE, eval=FALSE--------------------- # # zen gene # idxTrack <- IdeogramTrack(genome = "dm6", chromosome = "chr3R") # # # get Exons for zen adjacent genes # queryExons$where[[1]]$value = zen_AdjacentGenes$Gene.downstreamIntergenicRegion.adjacentGenes.symbol # zen.down.Exons = runQuery(im.fly, queryExons) # # queryExons$where[[1]]$value = zen_AdjacentGenes$Gene.upstreamIntergenicRegion.adjacentGenes.symbol # zen.up.Exons = runQuery(im.fly, queryExons) # # # get strand for zen ROI genes # zen.strand = gsub( # pattern = "-1", # replacement = "-", # x = c( # zen.Exons$Gene.exons.chromosomeLocation.strand # ) # ) # # zen.adjacent.strand = gsub( # pattern = "-1", # replacement = "-", # x = c( # zen.down.Exons$Gene.exons.chromosomeLocation.strand, # zen.up.Exons$Gene.exons.chromosomeLocation.strand # ) # ) # # # index for zen gene_info # ind.gi = which(gene_info$Gene.symbol == "zen") # # # zen data.frame for GeneRegionTrack # zenTrack = data.frame( # chromosome = "chr3R", # start = as.numeric(c( # zen.Exons$Gene.exons.chromosomeLocation.start # )), # end = as.numeric(c( # zen.Exons$Gene.exons.chromosomeLocation.end # )), # strand = zen.strand, # feature = "protein-coding", # gene = gene_info[ind.gi,1], # exon = c( # zen.Exons$Gene.exons.primaryIdentifier # ), # transcript = "zen" # ) # # zenTrack <- GeneRegionTrack(zenTrack, # genome = "dm6", # chromosome = "chr3R", # name = "zen", # background.title = "brown", # transcriptAnnotation = "transcript" # ) # # # zen Adjacent genes data.frame for GeneRegionTrack # zenAdjacentTrack = data.frame( # chromosome = "chr3R", # start = as.numeric(c( # zen.down.Exons$Gene.exons.chromosomeLocation.start, # zen.up.Exons$Gene.exons.chromosomeLocation.start # )), # end = as.numeric(c( # zen.down.Exons$Gene.exons.chromosomeLocation.end, # zen.up.Exons$Gene.exons.chromosomeLocation.end # )), # strand = zen.adjacent.strand, # exon = c( # zen.down.Exons$Gene.exons.primaryIdentifier, # zen.up.Exons$Gene.exons.primaryIdentifier # ), # transcript = c( # rep(zen_AdjacentGenes$Gene.downstreamIntergenicRegion.adjacentGenes.symbol,nrow(zen.down.Exons)), # rep(zen_AdjacentGenes$Gene.upstreamIntergenicRegion.adjacentGenes.symbol, nrow(zen.up.Exons)) # ) # ) # # zenAdjacentTrack <- GeneRegionTrack(zenAdjacentTrack, # genome = "dm6", # chromosome = "chr3R", # name = "zen Adjacent Genes", # transcriptAnnotation = "transcript", # background.title = "brown" # ) # # # zen ROI TFbinding sites for GeneRegionTrack # # zen.ROI.TFBindingSites.track = data.frame( # chromosome = paste0("chr",zen.ROI.TFBindingSites$TFBindingSite.chromosome.primaryIdentifier), # start = as.numeric(zen.ROI.TFBindingSites$TFBindingSite.chromosomeLocation.start), # end = as.numeric(zen.ROI.TFBindingSites$TFBindingSite.chromosomeLocation.end), # symbol = zen.ROI.TFBindingSites$TFBindingSite.factor.name # ) # # zen.ROI.TFBindingSites.track = GeneRegionTrack( # zen.ROI.TFBindingSites.track, # genome = "dm6", # chromosome = "chr3R", # name = "TFs", # background.title = "darkgreen", # fill = "salmon" # ) # # # zen ROI Regulatory Regions for GeneRegionTrack # # zen.ROI.RRLocations.track = data.frame( # chromosome = paste0("chr",zen.ROI.RRLocations$RegulatoryRegion.chromosome.primaryIdentifier), # start = as.numeric(zen.ROI.RRLocations$RegulatoryRegion.chromosomeLocation.start), # end = as.numeric(zen.ROI.RRLocations$RegulatoryRegion.chromosomeLocation.end), # symbol = zen.ROI.RRLocations$RegulatoryRegion.primaryIdentifier # ) # # zen.ROI.RRLocations.track = GeneRegionTrack( # zen.ROI.RRLocations.track, # genome = "dm6", # chromosome = "chr3R", # name = "Regulatory Regions", # background.title = "darkgreen", # fill = "lightblue" # ) # # # plotTracks(list(idxTrack, # axTrack, # zenTrack, # zenAdjacentTrack, # zen.ROI.TFBindingSites.track, # zen.ROI.RRLocations.track, # zen.ROI.cpgIslands, # zen.ROI.conservation, # zen.ROI.gcContent), # showTitle = T, # shape = "arrow") ## ----eve_vis, warning=FALSE, message=FALSE, eval=FALSE--------------------- # # eve gene # idxTrack <- IdeogramTrack(genome = "dm6", chromosome = "chr2R") # # # get Exons for eve overlapping genes # queryExons$where[[1]]$value = eve_OverlappingGenes$Gene.overlappingFeatures.symbol # eve.over.Exons = runQuery(im.fly, queryExons) # # # # get strand for eve ROI genes # eve.strand = gsub( # pattern = "1", # replacement = "+", # x = c( # eve.Exons$Gene.exons.chromosomeLocation.strand # ) # ) # # eve.over.strand = gsub( # pattern = "-1", # replacement = "-", # x = c( # eve.over.Exons$Gene.exons.chromosomeLocation.strand # ) # ) # # # index for eve gene_info # ind.gi = which(gene_info$Gene.symbol == "eve") # # # eve data.frame for GeneRegionTrack # eveTrack = data.frame( # chromosome = "chr2R", # start = as.numeric(c( # eve.Exons$Gene.exons.chromosomeLocation.start # )), # end = as.numeric(c( # eve.Exons$Gene.exons.chromosomeLocation.end # )), # strand = eve.strand, # feature = "protein-coding", # gene = gene_info[ind.gi,1], # exon = c( # eve.Exons$Gene.exons.primaryIdentifier # ), # transcript = "eve" # ) # # eveTrack <- GeneRegionTrack(eveTrack, # genome = "dm6", # chromosome = "chr2R", # name = "eve", # background.title = "brown", # transcriptAnnotation = "transcript" # ) # # # eve Adjacent genes data.frame for GeneRegionTrack # eveOverlapTrack = data.frame( # chromosome = "chr2R", # start = as.numeric(c( # eve.over.Exons$Gene.exons.chromosomeLocation.start # )), # end = as.numeric(c( # eve.over.Exons$Gene.exons.chromosomeLocation.end # )), # strand = eve.over.strand, # exon = c( # eve.over.Exons$Gene.exons.primaryIdentifier # ), # transcript = c( # eve_OverlappingGenes$Gene.overlappingFeatures.symbol # ) # ) # # eveOverlapTrack <- GeneRegionTrack(eveOverlapTrack, # genome = "dm6", # chromosome = "chr2R", # name = "eve Overlapping Genes", # transcriptAnnotation = "transcript", # background.title = "brown" # ) # # # eve ROI TFbinding sites for GeneRegionTrack # # eve.ROI.TFBindingSites.track = data.frame( # chromosome = paste0("chr",eve.ROI.TFBindingSites$TFBindingSite.chromosome.primaryIdentifier), # start = as.numeric(eve.ROI.TFBindingSites$TFBindingSite.chromosomeLocation.start), # end = as.numeric(eve.ROI.TFBindingSites$TFBindingSite.chromosomeLocation.end), # symbol = eve.ROI.TFBindingSites$TFBindingSite.factor.name # ) # # eve.ROI.TFBindingSites.track = GeneRegionTrack( # eve.ROI.TFBindingSites.track, # genome = "dm6", # chromosome = "chr2R", # name = "TFs", # background.title = "darkgreen", # fill = "salmon" # ) # # # eve ROI Regulatory Regions for GeneRegionTrack # # eve.ROI.RRLocations.track = data.frame( # chromosome = paste0("chr",eve.ROI.RRLocations$RegulatoryRegion.chromosome.primaryIdentifier), # start = as.numeric(eve.ROI.RRLocations$RegulatoryRegion.chromosomeLocation.start), # end = as.numeric(eve.ROI.RRLocations$RegulatoryRegion.chromosomeLocation.end), # symbol = eve.ROI.RRLocations$RegulatoryRegion.primaryIdentifier # ) # # eve.ROI.RRLocations.track = GeneRegionTrack( # eve.ROI.RRLocations.track, # genome = "dm6", # chromosome = "chr2R", # name = "Regulatory Regions", # background.title = "darkgreen", # fill = "lightblue" # ) # # # plotTracks(list(idxTrack, # axTrack, # eveTrack, # eveOverlapTrack, # eve.ROI.TFBindingSites.track, # eve.ROI.RRLocations.track, # eve.ROI.cpgIslands, # eve.ROI.conservation, # eve.ROI.gcContent), # showTitle = T, # shape = "arrow") ## ----r_vis, warning=FALSE, message=FALSE, eval=FALSE----------------------- # # r gene # idxTrack <- IdeogramTrack(genome = "dm6", chromosome = "chrX") # # # get Exons for r adjacent genes # queryExons$where[[1]]$value = r_AdjacentGenes$Gene.downstreamIntergenicRegion.adjacentGenes.symbol # r.down.Exons = runQuery(im.fly, queryExons) # # queryExons$where[[1]]$value = r_AdjacentGenes$Gene.upstreamIntergenicRegion.adjacentGenes.symbol # r.up.Exons = runQuery(im.fly, queryExons) # # # get Exons for r adjacent genes # queryExons$where[[1]]$value = r_OverlappingGenes$Gene.overlappingFeatures.symbol # r.over.Exons = runQuery(im.fly, queryExons) # # # get strand for r ROI genes # r.strand = gsub( # pattern = "1", # replacement = "+", # x = c( # r.Exons$Gene.exons.chromosomeLocation.strand # ) # ) # # r.adjacent.strand = gsub( # pattern = "-1", # replacement = "-", # x = c( # r.down.Exons$Gene.exons.chromosomeLocation.strand, # r.up.Exons$Gene.exons.chromosomeLocation.strand # ) # ) # # r.over.strand = gsub( # pattern = "-1", # replacement = "-", # x = c( # r.over.Exons$Gene.exons.chromosomeLocation.strand # ) # ) # # # index for r gene_info # ind.gi = which(gene_info$Gene.symbol == "r") # # # r data.frame for GeneRegionTrack # rTrack = data.frame( # chromosome = "chrX", # start = as.numeric(c( # r.Exons$Gene.exons.chromosomeLocation.start # )), # end = as.numeric(c( # r.Exons$Gene.exons.chromosomeLocation.end # )), # strand = r.strand, # feature = "protein-coding", # gene = gene_info[ind.gi,1], # exon = c( # r.Exons$Gene.exons.primaryIdentifier # ), # transcript = "r" # ) # # rTrack <- GeneRegionTrack(rTrack, # genome = "dm6", # chromosome = "chrX", # name = "r", # background.title = "brown", # transcriptAnnotation = "transcript" # ) # # # r Adjacent genes data.frame for GeneRegionTrack # rAdjacentTrack = data.frame( # chromosome = "chrX", # start = as.numeric(c( # r.down.Exons$Gene.exons.chromosomeLocation.start, # r.up.Exons$Gene.exons.chromosomeLocation.start # )), # end = as.numeric(c( # r.down.Exons$Gene.exons.chromosomeLocation.end, # r.up.Exons$Gene.exons.chromosomeLocation.end # )), # strand = r.adjacent.strand, # exon = c( # r.down.Exons$Gene.exons.primaryIdentifier, # r.up.Exons$Gene.exons.primaryIdentifier # ), # transcript = c( # rep(r_AdjacentGenes$Gene.downstreamIntergenicRegion.adjacentGenes.symbol,nrow(r.down.Exons)), # rep(r_AdjacentGenes$Gene.upstreamIntergenicRegion.adjacentGenes.symbol, nrow(r.up.Exons)) # ) # ) # # rAdjacentTrack <- GeneRegionTrack(rAdjacentTrack, # genome = "dm6", # chromosome = "chrX", # name = "r Adjacent Genes", # transcriptAnnotation = "transcript", # background.title = "brown" # ) # # # r Overlapping genes data.frame for GeneRegionTrack # rOverTrack = data.frame( # chromosome = "chrX", # start = as.numeric(c( # r.over.Exons$Gene.exons.chromosomeLocation.start # )), # end = as.numeric(c( # r.over.Exons$Gene.exons.chromosomeLocation.end # )), # strand = r.over.strand, # exon = c( # r.over.Exons$Gene.exons.primaryIdentifier # ), # transcript = c( # r_OverlappingGenes$Gene.overlappingFeatures.symbol # ) # ) # # rOverTrack <- GeneRegionTrack(rOverTrack, # genome = "dm6", # chromosome = "chrX", # name = "r Overlapping Genes", # transcriptAnnotation = "transcript", # background.title = "brown" # ) # # # r ROI TFbinding sites for GeneRegionTrack # is.null(r.ROI.TFBindingSites) # # # r ROI Regulatory Regions for GeneRegionTrack # is.null(r.ROI.RRLocations) # # plotTracks(list(idxTrack, # axTrack, # rTrack, # rAdjacentTrack, # rOverTrack, # r.ROI.cpgIslands, # r.ROI.conservation, # r.ROI.gcContent), # showTitle = T, # shape = "arrow") ## ----sessioInfo------------------------------------------------------------ sessionInfo()