# # # R代码从装饰图案的cpvSNP来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:风格# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # BiocStyle::乳胶()# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:loadLibrariesAndData # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(cpvSNP)数据(geneSetAnalysis)名称(geneSetAnalysis) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:createArrayData # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # arrayDataGR <——createArrayData (geneSetAnalysis [[“arrayData”]], positionName =“位置”)类(arrayDataGR) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:geneSets # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # geneSets <——geneSetAnalysis [[“geneSets”]] geneSets长度(geneSets)头(geneIds (geneSets[[1]]))细节(geneSets[[1]])头(geneIds (geneSets[[2]])) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:geneToSNPList # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb < - TxDb.Hsapiens.UCSC.hg19。knownGene genesHg19 (txdb) snpsGSC < < -基因——geneToSNPList (geneSets, arrayDataGR genesHg19)类(snpsGSC) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:readyToRun # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # arrayDataGR snpsGSC # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:它的# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #它<——geneSetAnalysis [[“indepSNPs”]]头(它)的(它的)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:createIndepP # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # pvals < - arrayDataGR $ P [。它的元素(arrayDataGR SNP美元,美元V1)]的名字(pvals) < - arrayDataGR SNP是美元。它的元素(arrayDataGR SNP美元,美元V1)]头(pvals) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:glossi # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #格蕾丝< - glossi (pvals snpsGSC)格蕾丝gRes2 <——glossi (pvals, snpsGSC [[1]]) gRes2 pValue(格蕾丝)degreesOfFreedom(格蕾丝)统计(格蕾丝)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:publishMultiple (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # pvals < - p。调整(unlist (pValue(格蕾丝)),方法=“黑洞”)图书馆(ReportingTools) # # # #报告< - HTMLReport(短=“cpvSNP_glossiResult”, # # title =“GLOSSI结果”,reportDirectory =“。/报告”)# #发布(geneSets、报告、注释。db = " org.Hs。如“# # setStats = unlist(统计(格蕾丝)),# # setPValues = pvals) # #完成(报告)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:人类基因组单体型图(eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #下载。文件(url = " http://hapmap.ncbi.nlm.nih.gov/genotypes/hapmap3_r3/plink_format/hapmap3_r3_b36_fwd.consensus.qc.poly.ped.gz " # #, # # destfile =“hapmap3_r3_b36_fwd.consensus.qc.poly.ped.gz”) # #下载。文件(url = " http://hapmap.ncbi.nlm.nih.gov/genotypes/hapmap3_r3/plink_format/hapmap3_r3_b36_fwd.consensus.qc.poly.map.gz " # #, # # destfile =“hapmap3_r3_b36_fwd.consensus.qc.poly.map.gz”) # #系统(“gunzip hapmap3_r3_b36_fwd.consensus.qc.poly.ped.gz”) # #系统(“gunzip hapmap3_r3_b36_fwd.consensus.qc.poly.map.gz”) # #系统(hapmap3_r3_b36_fwd.consensus.qc“叮铃声——文件。聚,铺床,对应1”)# # # #基因族群< -阅读。叮铃声(床,荡妇,fam) # #基因族群基因型# #美元头(基因族群地图美元)# # x < -基因族群[,is.element(基因族群地图snp.name美元,c (geneIds (snpsGSC [[2]])))) # # ldMat < - ld (x, y = x,统计=“R.squared”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块12号:拉斯维加斯(eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ldMat < - geneSetAnalysis [[“ldMat”]] # # vr < - - - - - -拉斯维加斯(snpsGSC [1], arrayDataGR, ldMat) # # vr # #总结(unlist (simulatedStats (vr))) # # # # pValue (vr) # # degreesOfFreedom (vr) # #统计(vr) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块13号:plotb # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # plotPvals(格蕾丝,主要=“GLOSSI假定值”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块14号:plot2 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # pvals < - $ P arrayDataGR名称(pvals) <——arrayDataGR SNP assocPvalBySetPlot美元(pvals, snpsGSC[[2]]) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量15:sessInfo # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # toLatex (sessionInfo()) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量16:resetOptions # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(提示=“>”,继续= " + ")