# #设置,包括= FALSE --------------------------------------------------- 库(knitr) # knitr: opts_knit美元集(根。dir = normalizePath("/Users/mbuljan/Documents/Paket_op/DominoEffect_radna/inst/doc")) #library(devtools) #knitr::opts_knit$set(根。dir = normalizePath(本月(“DominoEffect "))) ## ---- eval = FALSE -------------------------------------------------------------- # 如果(!需要(“BiocManager”))# install.packages (BiocManager) # BiocManager::安装(“DominoEffect ") ## ----------------------------------------------------------------------------- 库(DominoEffect ) ## ----------------------------------------------------------------------------- 数据(“TestData”,包=“DominoEffect”)的数据(“SnpData”,包= " DominoEffect ")数据(“DominoData”,包= " DominoEffect ") ## ---- eval = FALSE -------------------------------------------------------------- # DominoEffect (TestData DominoData SnpData ) ## ---- eval = FALSE -------------------------------------------------------------- # mutation_dataset =阅读。table ("user_file_with_mutations.txt"， header = T) # gene_data = read。table ("user_ensembl_gene_list.txt"， header = T) # snp_data = read。表(“user_population_SNPs_with_frequency.txt”,标题= T ) ## ---- 消息= FALSE,结果= "隐藏 "--------------------------------------- hotspot_mutations < DominoEffect (mutation_dataset = TestData gene_data = DominoData snp_data = SnpData ) ## ---- eval = FALSE ------------------------------------------------------------- # 数据(“TestData”,包= " DominoEffect ") ## ---- 回声= FALSE ------------------------------------------------------------ kable(头(TestData),row.names = FALSE ) ## ---- 回声= FALSE ------------------------------------------------------------ kable(头(hotspot_mutations), row.names = FALSE ) ## ---- eval = FALSE ------------------------------------------------------------ # hotspot_mutations < DominoEffect (mutation_dataset、gene_data snp_data, min_n_muts, MAF_thresh, flanking_region,泊松。用力推,百分比。用力推,比率。用力推,方法,write_to_file ) ## ----------------------------------------------------------------------------- min_n_muts < - 5 ## ----------------------------------------------------------------------------- 加器。用力推< - 0.01 ## ----------------------------------------------------------------------------- flanking_region < - c(200、300)flanking_region < - c (300 ) ## ----------------------------------------------------------------------------- 泊松。用力推< - 0.01 ## ----------------------------------------------------------------------------- 百分比。用力推< - 0.15 ## ----------------------------------------------------------------------------- 比率。用力推< - 40 ## ----------------------------------------------------------------------------- 方法= "百分比 " ## ---- eval = FALSE ------------------------------------------------------------ # write_to_file = "是的 " ## ---- 消息= FALSE,结果=“隐藏”,eval = FALSE ------------------------- # hotspot_mutations < - DominoEffect (mutation_dataset = TestData # gene_data = DominoData,snp_data = SnpData ) ## ---- 消息= FALSE --------------------------------------------------------- hotspot_mutations < identify_hotspots (mutation_dataset = TestData gene_data = DominoData snp_data = SnpData min_n_muts = 5, MAF_thresh = 0.01, flanking_region = c(200、300),泊松。THR = 0.01，百分比。THR = 0.15，比率。thr = 45, approach = "percentage") ## ---- message = FALSE, eval = FALSE------------------------------------------- # results_w_annotations <- map_to_func_elem(hotspot_mutations, # write_to_file = "NO", # ens_release = "73") ## ---- echo = FALSE------------------------------------------------------------ kable(head(DominoData), row.names = FALSE) ## ---- echo = FALSE------------------------------------------------------------ kable(head(SnpData), row.names = FALSE) ## ---- echo = FALSE------------------------------------------------------------ hotspot_mutations.GPo <- GPo_of_hotspots(hotspot_mutations) head(hotspot_mutations.GPo) ## ----------------------------------------------------------------------------- sessionInfo()