## ----负载风格，警告= false，echo = false，message = false，结果=“ hide” ------库（biocStyle）## ----软件包，inclage inclage = false-----------------------------------------------------------------------库（YAPSA）库（生物弦）库（bsgenome.hsapiens.ucsc.hg19）库（knitr）opts_chunk $ set（echo = true）opts_chunk $ set（fig.show ='asis'------------------------------------------------------------------------------------数据（SIGS）数据（截止）数据（“淋巴女性2013_mutcat_df”）current_cutoff_vector <-cutoffcosmicvalid_abs_df [6，] ## --------------------------------------------------------------------------- lymphoma_COSMIC_listsList <- LCD_complex_cutoff_combined( in_mutation_catalogue_df = lymphomaNature2013_mutCat_df, in_cutoff_vector = current_cutoff_vector, in_signatures_df = AlexCosmicValid_sig_df, in_sig_ind_df = AlexCosmicValid_sigInd_df) ## ----subrgroupAnnotation----------------------------------------------------------数据（淋巴瘤_PID）colnames（淋巴瘤_PID_DF）< - “亚组”淋巴瘤_PID__PID_df $ pid <-rownames（lymphoma_pid_df）cosmic_subgroups_df <-sake_subgroups_df（lymphoma_pid_df，lymphoma_cosmic_listslistslist $ cohort $ cohort $ cohort $ eacposures $ eacposures $ eacposures $ eacposures）-------------------------------------------“暴露于SNV突变签名” ## ---- exposurescutoffs，警告= false，图.width = 8，图。，echo = false ------------------------------------------------------------------------------------------------------------------------------------------------------------------上限< - “暴露于突变签名的置信区间计算” ## ---- computeci，echo = true，警告= false----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------完整_df <-variateexp（in_catalogue_df = lymphomanature2013_mutcat_df，in_sig_df = lymphoma_cosmic_listslist $ cohort $ cohort $，，，，in_delta = 0.4）## ---------------------------------------------------------------------------------------------------------------------------（完整_df，12）## ---- plotci，echo = true，parning = false，fig.width = 17，图。 COSMIC_subgroups_df, in_sigInd_df = lymphoma_COSMIC_listsList$cohort$out_sig_ind_df)