source("http://bioconductor.org/biocLite.R") biocLite("biomaRt") biocLite("GenomeGraphs") biocLite("annotate") biocLite("hgu95av2.db") biocLite("GO.db") library("annotate") library("hgu95av2.db") library("GO.db") vignette(package="annotate") vignette("GOusage") library(help="hgu95av2.db") get("F5",hgu95av2ALIAS2PROBE) get("AGT", hgu95av2ALIAS2PROBE) get("35245_at",hgu95av2GO) get("GO:0007155",hgu95av2GO2PROBE) #biocLite("biomaRt") library("biomaRt") human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") listAttributes(human) getBM(attributes="go_id",filters="hgnc_symbol", values="F5",mart=human) listFilters(human) getBM(attributes="hgnc_symbol", filters="go_id",values="GO:0007155",mart=human) ### 4. #biocLite("GenomeGraphs") library("GenomeGraphs") gene <- makeGene(id = "AGT", type = "hgnc_symbol", biomart = human) transcript<-makeTranscript(id="AGT",type="hgnc_symbol", biomart=human) ideogram <- makeIdeogram(chromosome ="1") gdPlot(list(ideogram,gene)) gdPlot(list(ideogram,gene,transcript)) minbase<-230000000 maxbase<-231000000 genesplus <- makeGeneRegion(start = minbase, end = maxbase, strand = "+", chromosome = "1", biomart = human) genesminus <- makeGeneRegion(start = minbase, end = maxbase, strand = "-", chromosome = "1", biomart = human) genomeAxis <- makeGenomeAxis(add53 = TRUE, add35 = TRUE) gdPlot(list(ideogram,genesplus,genomeAxis,genesminus,gene)) ### getBM(attributes=c("chromosome_name","start_position","end_position"),filters="mgi_symbol",values="Cxcl5",mart=mouse) horse = useMart("ensembl", dataset = "ecaballus_gene_ensembl") listFilters(horse) getBM("GYS1", filters="wikigene_name", attributes="chromosome_name",mart=horse) stckl = useMart("ensembl", dataset = "gaculeatus_gene_ensembl") listFilters(stckl)