# # # R代码从装饰图案的QuartPAC来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:例二# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(QuartPAC) #读取突变数据mutation_files < -列表(执行(“extdata”、“HFE_Q30201_MutationOutput。txt”,包= " QuartPAC”),执行(“extdata”、“B2M_P61769_MutationOutput。txt”,包= " QuartPAC ")) uniprots < -列表(“Q30201”、“P61769”)突变。数据< - getMutations (mutation_files = mutation_files uniprots = uniprots) # pdb文件读取pdb。位置< -“https://files.rcsb.org/view/1A6Z.pdb”组装。位置< -“https://files.rcsb.org/download/1A6Z.pdb1”结构。< - makeAlignedSuperStructure (pdb数据。位置,assembly.location) #执行分析#我们使用非常高α水平没有多重比较调整#确保每个方法提供了显示了结果。通常使用#降低α减少偏移。quart_results < - quartCluster(突变。数据结构。数据,执行。ipac = " Y ",执行。graphpac = " Y ",执行。spacepac = " Y ",创造。地图= " Y ",α=。3,MultComp =“没有”,图。Title =“MDS映射到一维空间”,半径。vector = c(1:3)) ################################################### ### code chunk number 2: Example2 ################################################### Plot.Protein.Linear(quart_results$graphpac$candidate.path, colCount = 10, title = "Protein Reordering to 1D Space via GraphPAC") ################################################### ### code chunk number 3: Example3 ################################################### #look at the results for the optimal sphere combinations under the SpacePAC approach #For clarity we only look at columns 3 - 8 which show the sphere centers. quart_results$spacepac$optimal.sphere[,3:8] #Find the atom with serial number 1265 required.row <- which(structural.data$aligned_structure$serial == 1265) #show the information for that atom structural.data$aligned_structure[required.row,] ################################################### ### code chunk number 4: Example4 ################################################### #look at the results for the first cluster shown by the ipac method quart_results$ipac #Find the atoms with serial numbers within the range of 2583 to 2846 required.rows <- which(structural.data$aligned_structure$serial %in% (2583:2846)) #show the information for those atoms structural.data$aligned_structure[required.rows,]