# #——style-knitr eval = TRUE,呼应= FALSE,结果= "飞机 "----------------------------- BiocStyle:乳胶 () ## ---- 包括= FALSE ------------------------------------------------------------------ 库(knitr) opts_chunk美元集(= TRUE结果一致,背景= " # f3f3ff " ) ## ---- 要求的事情 ---------------------------------------------------------------------------- 库(“花边”)数据(longitudinal_sc_variants)名称(longitudinal_sc_variants) # #——req_se ------------------------------------------------------------------------- 库(“SummarizedExperiment attach.required = FALSE) T1 = t (longitudinal_sc_variants [[1]]) T2 = t (longitudinal_sc_variants [[2]]) T3 = t (longitudinal_sc_variants [[3]]) T4 = t (longitudinal_sc_variants [[4]])concat_time_point = cbind(T1,T2,T3,T4) TimePointLabes = c(rep("T1"， ncol(T1))， rep("T2"， ncol(T2))， rep("T3"， ncol(T3))， rep("T4"， ncol(T4)))， longitude al_se = summarizeexperiment (assays = concat_time_point，colData = data.frame(计算= TimePointLabes)打印(longitudinal_SE) # #——example_weights ---------------------------------------------------------------- lik_weights = c(0.2308772, 0.2554386, 0.2701754, 0.2435088) # #——example_error_rates ------------------------------------------------------------ α=列表()α[[1]]= c(0.02, 0.01, 0.01, 0.01)α[[2]]= c(0.10, 0.05, 0.05, 0.05)β=列表()β[[1]]= c(0.10, 0.05, 0.05, 0.05)β[[2]]= c(0.10, 0.05, 0.05, 0.05)头(α)头(β)# #----example_inference-------------------------------------------------------------- inference = LACE(D = longitudinal_sc_variants, lik_w = lik_weights, alpha = alpha, beta = beta, keep_equivalent = TRUE, num_rs = 5, num_iter = 10, n_try_bs = 5, num_processes = NA, seed = 12345, verbose = FALSE) ## ----example_inference_full--------------------------------------------------------- data(inference) print(names(inference)) ## ----example_plot------------------------------------------------------------------- clone_labels = c("ARPC2","PRAME","HNRNPC","COL1A2","RPL5","CCT8") longitudinal.tree = longitudinal.tree.plot(inference = inference, labels_show = "clones", clone_labels = clone_labels, legend_position = "topright") ## ----sessioninfo,results='asis',echo=FALSE------------------------------------------ toLatex(sessionInfo())