# # # R代码从装饰图案的package_vignettes来源。Snw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:package_vignettes。Snw: 33节(eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(哥特式)数据(lymphoid_chr20_paired_filtered) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:package_vignettes。Snw: 79 - 84 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # dirPath =系统。文件(“extdata”,包=“HiCDataLymphoblast”) # # fileName1 =列表。文件(dirPath full.names = TRUE) [1] # # fileName2 =列表。文件(dirPath full.names = TRUE) [2] # # = pairReads配对(fileName1、fileName2 sampleName =“lymphoid_chr20”, # # DUPLICATETHRESHOLD = 1,文件类型=“表”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:package_vignettes。Snw: 91 - 96 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据映射(lymphoid_chr20_paired_filtered) # # = mapReadsToRestrictionSites(过滤、sampleName =“lymphoid_chr20”, # # BSgenomeName = " BSgenome.Hsapiens.UCSC。hg18基因组”,# # = BSgenome.Hsapiens.UCSC。hg18 # # restrictionSite =“^ AGCTT”,酶=“HindIII”,平行= FALSE,核= 1)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:package_vignettes。Snw: 103 - 111 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # dirPath =系统。文件(“extdata”,包=“HiCDataLymphoblast”) # # fileName1 =列表。文件(dirPath full.names = TRUE) [1] # # fileName2 =列表。文件(dirPath full.names = TRUE) [2] # # binom =哥特式(fileName1、fileName2 sampleName =“lymphoid_chr20”, # # res = 1000000, BSgenomeName = " BSgenome.Hsapiens.UCSC。hg18基因组”,# # = BSgenome.Hsapiens.UCSC。hg18 # # restrictionSite =“^ AGCTT”,酶=“HindIII cistrans =“所有”,filterdist = 10000, # # DUPLICATETHRESHOLD = 1,文件类型=“表”,平行= FALSE,核= NULL) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:package_vignettes。Snw: 114 - 119 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # dirPath < -系统。文件(“extdata”,包=“HiCDataLymphoblast”) < - # #文件名列表。文件(dirPath full.names = TRUE) [4] # # restrictionFile < -列表。文件(dirPath full.names = TRUE) [3] # # binom = GOTHiChicup(文件名,sampleName = lymphoid_chr20, res = 1000000, # # restrictionFile, cistrans =‘所有’,平行= FALSE,核= NULL)