## ----loadStyle, warning=FALSE, echo=FALSE, message=FALSE, results="hide"------ library(BiocStyle) ## ----packages, include=FALSE-------------------------------------------------- library(YAPSA) library(knitr) library(gridExtra) library(dplyr) opts_chunk$set(echo=TRUE) opts_chunk$set(fig.show='asis') ## ----loadSignatures----------------------------------------------------------- data(sigs) data(sigs_pcawg) ## ----loadCutoffs-------------------------------------------------------------- data(cutoffs) data(cutoffs_pcawg) ## ----cutoffExample------------------------------------------------------------ data(cutoffs) current_cutoff_vector <- cutoffCosmicValid_abs_df[6, ] current_cutoff_vector ## ----loadData----------------------------------------------------------------- data(lymphomaNature2013_mutCat_df) ## ----setVariables------------------------------------------------------------- current_sig_df <- AlexCosmicValid_sig_df current_sigInd_df <- AlexCosmicValid_sigInd_df ## ----cutoffVector------------------------------------------------------------- current_cutoff_vector <- rep(0, dim(AlexCosmicValid_sig_df)[2]) ## ----lymphomaCohortLCD_results------------------------------------------------ lymphoma_COSMIC_zero_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) ## ----subrgroupAnnotation------------------------------------------------------ data(lymphoma_PID) colnames(lymphoma_PID_df) <- "SUBGROUP" lymphoma_PID_df$PID <- rownames(lymphoma_PID_df) COSMIC_subgroups_df <- make_subgroups_df(lymphoma_PID_df, lymphoma_COSMIC_zero_listsList$cohort$exposures) ## ----captionBarplot2, echo=FALSE---------------------------------------------- cap <- "Absoute exposures of the COSMIC signatures in the lymphoma mutational catalogs, signature-specific cutoffs with a cost factor of 6 used for the LCD" ## ----exposuresZero, warning=FALSE, fig.width=8, fig.height=6, fig.cap = cap---- result_cohort <- lymphoma_COSMIC_zero_listsList$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 <- "Absolute exposures of the COSMIC signatures in the lymphoma mutational catalogs, signature-specific cutoffs with a cost factor of 6 used for the LCD" ## ----exposuresCutoffs, warning=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)