# # # R代码从装饰图案的r3Cseq来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:设置# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(宽度= 60)olocale = Sys.setlocale (locale =“C”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:r3Cseq。Rnw: 208 - 209 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(r3Cseq) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:r3Cseq。Rnw: 212 - 214 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # (Myb_prom_FL)数据(Myb_prom_FB) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:r3Cseq。Rnw: 233 - 237 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # my3Cseq。obj < - (r3Cseq organismName = mm9, isControlInvolved = TRUE, viewpoint_chromosome = chr10, viewpoint_primer_forward = TCTTTGTTTGATGGCATCTGTT, viewpoint_primer_reverse = AAAGGGGAGGAGAAGGAGGT, expLabel =“Myb_prom_FL contrLabel =“MYb_prom_FB restrictionEnzyme = HindIII) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:r3Cseq。Rnw: 241 - 243 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # expRawData < exp (my3Cseq.obj)。农庄contrRawData (my3Cseq.obj) <来讲。农庄# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:r3Cseq。Rnw: 246 - 247 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # my3Cseq。obj # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:r3Cseq。Rnw: 252 - 253 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # getReadCountPerRestrictionFragment (my3Cseq.obj) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:r3Cseq。Rnw: 261 - 262 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # calculateRPM (my3Cseq.obj) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:r3Cseq。Rnw: 266 - 267 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # getInteractions (my3Cseq.obj,富兰克林·德兰诺·罗斯福= 0.05)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:r3Cseq。Rnw: 272 - 274 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # fetal.liver.interactions < -expInteractionRegions (my3Cseq.obj) fetal.liver.interactions # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:r3Cseq。Rnw: 277 - 279 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # fetal.brain.interactions < -contrInteractionRegions (my3Cseq.obj) fetal.brain.interactions # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块12号:r3Cseq。Rnw:284-286 ################################################### viewpoint<-getViewpoint(my3Cseq.obj) viewpoint ################################################### ### code chunk number 13: plotOverviewInteractions ################################################### plotOverviewInteractions(my3Cseq.obj) ################################################### ### code chunk number 14: plotInteractionsNearViewpoint ################################################### plotInteractionsNearViewpoint(my3Cseq.obj) ################################################### ### code chunk number 15: plotInteractionsPerChromosome ################################################### plotInteractionsPerChromosome(my3Cseq.obj,"chr10") ################################################### ### code chunk number 16: r3Cseq.Rnw:335-336 ################################################### #plotDomainogramNearViewpoint(my3Cseq.obj) ################################################### ### code chunk number 17: r3Cseq.Rnw:341-343 ################################################### detected_genes<-getExpInteractionsInRefseq(my3Cseq.obj) head(detected_genes) ################################################### ### code chunk number 18: r3Cseq.Rnw:349-350 ################################################### #export3Cseq2bedGraph(my3Cseq.obj) ################################################### ### code chunk number 19: r3Cseq.Rnw:358-359 ################################################### #generate3CseqReport(my3Cseq.obj) ################################################### ### code chunk number 20: r3Cseq.Rnw:376-377 ################################################### sessionInfo()