# # # R代码从装饰图案的HiC_analysis来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:风格# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # BiocStyle::乳胶(use.unsrturl = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:头# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #需要类似(HiTC)需要(HiCDataHumanIMR90)数据(Dixon2012_IMR90)显示(hic_imr90_40)类(intdata (hic_imr90_40 chr1chr1)美元)object.size (hic_imr90_40) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:描述# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #显示数据显示(hic_imr90_40) # #是我的数据完整(即由内部+相关的国际米兰染色体地图)赋予isComplete (hic_imr90_40) # #请注意,一个完整的对象不一定是成对# # (chr1-chr2和chr2-chr1存储?)isPairwise染色体(hic_imr90_40) # # ?seqlevels (hic_imr90_40) # #细节给定映射细节(hic_imr90_40 chr6chr6美元)# #描述性统计负责人(总结(hic_imr90_40)) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:plot1 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #回到一个更小的数据集(chr21 22 X)在低分辨率sset < -减少(hic_imr90_40装备= c (“chr5”、“chr6”,“chr7”)) imr90_500 < - HTClist (mclapply (sset、binningC binsize = 500000,垃圾箱。调整= FALSE,方法= "和",步骤= 1))mapC (imr90_500) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:plot2 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # mapC (forcePairwise (imr90_500) maxrange = 200) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:resFrag # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #例X染色体上# #农庄后限制片段HindIII消化resFrag <——getRestrictionFragmentsPerChromosome (resSite =“AAGCTT overhangs5 = 1,染色体=“chr6 genomePack =“BSgenome.Hsapiens.UCSC.hg18”) resFrag # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:annot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #的基因组功能注释LGF正常化# # 6号染色体上的例子# #负载mappability跟踪要求(rtracklayer) # # map_hg18 < -进口(“wgEncodeCrgMapabilityAlign100mer_chr6.bw”,格式=“大佬”)map_hg18 < -零cutSites < getAnnotatedRestrictionSites (resSite =“AAGCTT overhangs5 = 1,染色体=“chr6 genomePack = " BSgenome.Hsapiens.UCSC。hg18”wingc = 200, mappability = map_hg18 winmap = 500)头(cutSites) # #高c对象的注释imr90_500_chr6annot <——setGenomicFeatures (imr90_500 chr6chr6美元,cutSites) y_intervals (imr90_500_chr6annot) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:normLGF (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # LGF正常化# # imr90_500_LGF <——normLGF (imr90_500_chr6annot) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:normICE # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # imr90_500_ICE < - normICE (imr90_500 max_iter = 10) mapC (HTClist (imr90_500_ICE chr6chr6美元),trim.range =。95年,col.pos = c(“白”,“橙色”,“红”,“黑”))# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:tads # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # hox <——extractRegion (hic_imr90_40 chr6chr6美元=“chr6”,从而向从= 50 e6, = 58 e6)情节(hox maxrange = 50, col.pos = c(“白”,“橙色”,“红”,“黑”))# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:di # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # di < -directionalityIndex (hox) barplot (di,坳= ifelse (di > 0,“darkred”,“暗绿色”))# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块12号:sessionInfo # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # toLatex (sessionInfo(),语言环境= FALSE)