# #——style-knitr eval = TRUE,呼应= FALSE,结果= "飞机 "-------------------- BiocStyle:乳胶 () ## -------------------------------------------------------------------------- suppressPackageStartupMessages({库(BUMHMM)图书馆(Biostrings)图书馆(SummarizedExperiment)}) ## -------------------------------------------------------------------------- 控制< - se (se $复制= =“控制”(试验(控制,的报道 ')) ## -------------------------------------------------------------------------- rowData(控制)[1:4 ,] ## -------------------------------------------------------------------------- colData(控制 ) ## -------------------------------------------------------------------------- pos < - 300试验(控制,“覆盖”)(pos, 1)测定(控制,dropoff_count) (pos, 1)测定(控制,dropoff_rate) [pos,1 ] ## -------------------------------------------------------------------------- 治疗< - se (se $复制= = "治疗"]试验(治疗,“覆盖”)(pos, 1)测定(治疗,dropoff_count) (pos, 1)测定(治疗,dropoff_rate) [pos 1 ] ## -------------------------------------------------------------------------- 数控< - Nt < - 3 t < - 1 nuclSelection < selectNuclPos (se,数控,新台币,t)列表(nuclSelection ) ## -------------------------------------------------------------------------- t (combn(数控2 )) ## -------------------------------------------------------------------------- 长度(nuclSelection analysedC美元[[1]])长度(nuclSelection analysedCT美元[[1 ]]) ## -------------------------------------------------------------------------- ## 每个复制应用原始的中位数下降率(化验(se, dropoff_rate), 2,中位数)# #规模下降率试验(,dropoff_rate) < - scaleDOR (se、nuclSelection、数控、Nt) # #中位数的比例下降率在每个复制应用(化验(se, dropoff_rate), 2,值 ) ## -------------------------------------------------------------------------- < - computeStretches延伸(se, t ) ## -------------------------------------------------------------------------- 头(拉伸)试验(,“dropoff_count”)[1748 ,] ## -------------------------------------------------------------------------- varStab < - stabiliseVariance (se、nuclSelection、数控、Nt) LDR_C < - varStab美元LDR_C LDR_CT < - varStab美元LDR_CT嘘(LDR_C休息= 30,主要= '零分布的贷款存款比率 ') ## -------------------------------------------------------------------------- nuclNum < < - - 3模式nuclPerm (nuclNum)模式 ## -------------------------------------------------------------------------- ## 提取DNA序列序列< -主题构成了rowData (se)诊断美元)(序列nuclPosition < - findPatternPos(模式、序列、' + ')模式[[1]](nuclPosition [[1 ]]) ## -------------------------------------------------------------------------- nuclPosition < -列表()nuclPosition [[1]] < - 1: nchar(序列)# #开始伸展nuclPosition[[1]][1] # #的拉伸nuclPosition[[1]][长度(nuclPosition [[1 ]])] ## -------------------------------------------------------------------------- 后验< computeProbs (LDR_C、LDR_CT、数控、Nt‘+’,nuclPosition, nuclSelection analysedC美元,nuclSelection analysedCT美元,延伸 ) ## -------------------------------------------------------------------------- (后验 ) ## -------------------------------------------------------------------------- shifted_posteriors < -矩阵(nrow =暗(屁股)[1],ncol = 1) shifted_posteriors[1:(长度(shifted_posteriors) - 1)) < -后验(2:暗(屁股)[1],2 ] ## -------------------------------------------------------------------------- 情节(shifted_posteriors xlab =“核苷酸位置”,ylab =修改的可能性,主要为18岁= ' BUMHMM输出DMS数据集 ') ## ---- eval = FALSE ------------------------------------------------------------ # ## 调用这个函数用额外的公差参数#后验< computeProbs (LDR_C、LDR_CT、数控、Nt‘+’,nuclPosition, # nuclSelection analysedC美元,nuclSelection analysedCT美元,#延伸,0.001 ) ## -------------------------------------------------------------------------- sessionInfo ()