# # # # 1。从AnnotationHub检索增强剂,单核苷酸多态性,基因坐标从TxDb。* # #;协调基因和染色体的名字# #库(AnnotationHub)中心< - AnnotationHub () hg19 <——中心(元数据(中心)基因组美元% % c (“hg19”、“GRCh37”)] # #增强剂,从编码BroadHmm跟踪# # -跟踪# # http://hgwdev.sdsc.edu/cgi-bin/hgTrackUi?的细节db = hg19&g = wgEncodeBroadHmm # # http://www.ncbi.nlm.nih.gov/pubmed/21441907嗯< - $ goldenpath.hg18.database.wgEncodeBroadHmm_0.0.1中心。RData # #错误“seqlengths”——“hg18”头衔,但实际上liftOver hg19库(BSgenome.Hsapiens.UCSC.hg19) seqlevels(嗯,力= TRUE) < - paste0(“空空”,一22)seqlengths(嗯)< - seqlengths (BSgenome.Hsapiens.UCSC.hg19)[名称(seqlengths(嗯)))基因组(嗯)<——“hg19”增强剂< - - - - - -嗯(grep(“剂”,嗯名称)美元)# # snp,例如,从chr1 CEU人口的snp < -查询(中心,“dbSNP。* 17。* CEU”)[[1]] # #真正的长度(1)单核苷酸多态性与单一ALT等位基因snp < - snp(宽度(snp) = = 1 & elementLengths (ALT (snp)) = = 1] seqlevelsStyle (SNPs) <——”UCSC基因组(SNPs) <——“hg19”# #基因坐标库(TxDb.Hsapiens.UCSC.hg19.knownGene) <基因-基因(TxDb.Hsapiens.UCSC.hg19.knownGene) <基因-基因(seqnames(基因)= = " chr17 "] # # # # 2。下载(大)保护跟踪从UCSC的床上文件,查询使用rtracklayer染色体1 # # # #库(rtracklayer) < url -粘贴(“http://hgdownload.cse.ucsc.edu/goldenPath/hg19”、“phastCons100way / hg19.100way.phastCons。bw”, 9 = " / ")桌子<——“~ / /资源/ hg19.100way.phastCons ismb - 2014。bw“# #下载。文件(url, dest) bw < - BigWigFile(桌子)chr17 < - (seqinfo (BigWigFile(桌子),“农庄”)(“chr17”)得分< -进口(bw, = chr17 =“NumericList”) [[“chr17”]] # # # # 4。子集snp的增强剂# # enhancerSnps < - subsetByOverlaps (SNPs,增强剂)# # # # 5。注释增强器单核苷酸多态性与进化保护得分# #分数< -分数(开始(enhancerSnps)) # #信息(enhancerSnps)美元分数< -分数(开始(enhancerSnps)) # # # # 6。找到最近的和distanceToNearest基因# #点击< - distanceToNearest (enhancerSnps,基因)df < - data.frame(=名字附近(基因)[subjectHits(点击)],距离= mcols美元(点击)距离,得分=分数,stringsAsFactors = FALSE)