## ----loadStyle, warning=FALSE, echo=FALSE, message=FALSE, results="hide"------ library(BiocStyle) ## ----packages, include=FALSE-------------------------------------------------- library(YAPSA) library(Biostrings) library(BSgenome.Hsapiens.UCSC.hg19) library(knitr) opts_chunk$set(echo=TRUE) opts_chunk$set(fig.show='asis') ## ----loadStoredSigData-------------------------------------------------------- data(sigs) data(cutoffs) data("lymphomaNature2013_mutCat_df") current_cutoff_vector <- cutoffCosmicValid_abs_df[6,] ## ----LCDwithCutoffs----------------------------------------------------------- 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------------------------------------------------------ data(lymphoma_PID) colnames(lymphoma_PID_df) <- "SUBGROUP" lymphoma_PID_df$PID <- rownames(lymphoma_PID_df) COSMIC_subgroups_df <- make_subgroups_df(lymphoma_PID_df, lymphoma_COSMIC_listsList$cohort$exposures) ## ----captionExposures, echo=FALSE--------------------------------------------- cap <- "Exposures to SNV mutational signatures" ## ----exposuresCutoffs, warning=FALSE, fig.width=8, fig.height=6, fig.cap= cap---- exposures_barplot( in_exposures_df = lymphoma_COSMIC_listsList$cohort$exposures, in_signatures_ind_df = lymphoma_COSMIC_listsList$cohort$out_sig_ind_df, in_subgroups_df = COSMIC_subgroups_df) ## ----captionCI, echo=FALSE---------------------------------------------------- cap <- "Confidence interval calculation for exposures to mutational signatures" ## ----computeCI, echo=TRUE, warning=FALSE-------------------------------------- complete_df <- variateExp( in_catalogue_df = lymphomaNature2013_mutCat_df, in_sig_df = lymphoma_COSMIC_listsList$cohort$signatures, in_exposures_df = lymphoma_COSMIC_listsList$cohort$exposures, in_sigLevel = 0.025, in_delta = 0.4) ## ----displayCompleteDf, echo=TRUE, warning=FALSE------------------------------ head(complete_df, 12) ## ----plotCI, echo=TRUE, warning=FALSE, fig.width=17, fig.height=15, fig.cap=cap---- plotExposuresConfidence( in_complete_df = complete_df, in_subgroups_df = COSMIC_subgroups_df, in_sigInd_df = lymphoma_COSMIC_listsList$cohort$out_sig_ind_df)