## ----loadStyle, warning=FALSE, echo=FALSE, message=FALSE, results="hide"------ library(BiocStyle) ## ----packages，包括= FALSE -------------------------------------------------- 库(YAPSA)库(knitr)图书馆(gridExtra)图书馆(dplyr) opts_chunk设置(echo = TRUE) opts_chunk设置美元(fig.show = '飞机 ') ## ---- loadSignatures ----------------------------------------------------------- 数据(团体)的数据(sigs_pcawg) # #——loadCutoffs -------------------------------------------------------------- 数据(达标)数据(cutoffs_pcawg) # #——cutoffExample ------------------------------------------------------------数据(达标)current_cutoff_vector < - cutoffCosmicValid_abs_df [6] current_cutoff_vector # #——loadData ----------------------------------------------------------------- 数据(lymphomaNature2013_mutCat_df) # #——setVariables ------------------------------------------------------------- current_sig_df < - AlexCosmicValid_sig_df current_sigInd_df < - AlexCosmicValid_sigInd_df # #——cutoffVector ------------------------------------------------------------- current_cutoff_vector < -代表(0,- LCD_complex_cutoff_combined(in_mutation_cataloggue_df = lymphomaNature2013_mutCat_df, in_cutoff_vector = current_cutoff_vector, in_signatures_df = current_sig_df，in_sig_ind_df = current_sigInd_df) # #——subrgroupAnnotation ------------------------------------------------------ 数据(lymphoma_PID) colnames (lymphoma_PID_df) < -“群”lymphoma_PID_df $ PID < - rownames (lymphoma_PID_df) COSMIC_subgroups_df <——make_subgroups_df (lymphoma_PID_df lymphoma_COSMIC_zero_listsList队列美元风险敞口)# #——captionBarplot2回声= FALSE ---------------------------------------------- 帽<——“Absoute曝光的宇宙签名淋巴瘤突变目录、## ----exposuresZero, warning=FALSE, fig.width=8, fig.height=6, fig.cap = cap---- result_cohort <- lympha_cosmic_zero_listslist $cohort exposures_barplot(in_exposures_df = result_cohort$exposures, in_signatures_ind_df = result_cohort$out_sig_ind_df，in_subgroups_df = COSMIC_subgroups_df) # #——setSignatureSpecificCutoffs ---------------------------------------------- current_cutoff_df < - cutoffCosmicValid_abs_df current_cost_factor < - 6 current_cutoff_vector < - current_cutoff_df [current_cost_factor ,] ## ---- LCDwithCutoffs ----------------------------------------------------------- lymphoma_COSMIC_listsList < LCD_complex_cutoff_combined (in_mutation_catalogue_df = lymphomaNature2013_mutCat_df in_cutoff_vector = current_cutoff_vector,in_signatures_df = current_sig_df, in_sig_ind_df = current_sigInd_df) ## ----captionBarplot, echo=FALSE----------------------------------------------- cap <-“在淋巴瘤突变目录中COSMIC签名的绝对曝光，用于LCD的成本因子为6的签名特定截断”## ----exposuresCutoffs，警告=FALSE, fig.width=8, fig.height=6，fig.cap= cap---- result_cohort <- lymphoma_COSMIC_listsList$cohort exposures_barplot(in_exposures_df = result_cohort$exposures, in_signatures_ind_df = result_cohort$out_sig_ind_df, in_subgroups_df = COSMIC_subgroups_df)