## ----style, eval=TRUE, echo = FALSE, results = 'asis'---------------------- BiocStyle::latex() ## ----load data, echo=FALSE, message=FALSE, paged.print=FALSE, results='asis'---- library(BOBaFIT) data("TCGA_BRCA_CN_segments") ## ----computeNormalChromosome, fig.show='hide', include=FALSE, results='hide'---- chr_list <- computeNormalChromosomes(segments = TCGA_BRCA_CN_segments, tolerance_val = 0.25) ## ----chr_list, results='asis'---------------------------------------------- chr_list ## ----chrlist plot, echo=FALSE, fig.height=10, fig.width=16----------------- chr_list <- computeNormalChromosomes(segments = TCGA_BRCA_CN_segments, tolerance_val = 0.25) ## ----DRrefit, eval=FALSE--------------------------------------------------- # results <- DRrefit (segments_chort = TCGA_BRCA_CN_segments, chrlist = chr_list) # ## ----DRrefit_test,include=FALSE-------------------------------------------- library(dplyr) samples <- TCGA_BRCA_CN_segments$ID %>% unique() sample_test <- samples[1:5] test <- TCGA_BRCA_CN_segments %>% filter(ID %in% sample_test) results <- DRrefit (segments_chort = test, chrlist = chr_list) ## ----call output PlotChrCluster code 1, eval=FALSE------------------------- # results$corrected_segments[1,] ## ----Call segments DRrefit 1, echo=FALSE, paged.print=TRUE----------------- table <- results$corrected_segments[1,] %>% select(chr,start,end, ID, arm, chrarm,CN,CN_corrected) knitr::kable(table,digits = 3) ## ----call output PlotChrCluster code 2, eval=FALSE------------------------- # results$report[1,] ## ----Call report DRrefit 2, echo=FALSE, paged.print=TRUE------------------- knitr::kable(results$report[1,]) ## ----DRrefit res----------------------------------------------------------- corrected_segments <- results$corrected_segments report <- results$report ## ----DRrefit_plot, eval=FALSE---------------------------------------------- # # the plot is diplayed on the R viewer # DRrefit_plot(corrected_segments = corrected_segments, # DRrefit_report = report, # plot_viewer = TRUE, # plot_save = FALSE ) # # # how to save the plot # DRrefit_plot(corrected_segments = corrected_segments, # DRrefit_report = report, # plot_save = TRUE, plot_format = "pdf", plot_path = "/my_path" ) ## ----DRrefit_plot 1, echo=FALSE, fig.height=7, fig.width=18---------------- report_s <- report[report$sample == "01428281-1653-4839-b5cf-167bc62eb147",] seg <- corrected_segments[corrected_segments$ID == "01428281-1653-4839-b5cf-167bc62eb147",] DRrefit_plot(corrected_segments = seg, DRrefit_report = report, plot_viewer = T ) ## ----DRrefit_plot 2, echo=FALSE, fig.height=7, fig.width=18---------------- report_s <- report[report$sample == "0941a978-c8aa-467b-8464-9f979d1f0418",] seg <- corrected_segments[corrected_segments$ID == "0941a978-c8aa-467b-8464-9f979d1f0418",] DRrefit_plot(corrected_segments = seg, DRrefit_report = report, plot_viewer = T ) ## ----PlotChrCluster, eval=FALSE-------------------------------------------- # Cluster <- PlotChrCluster(segs = TCGA_BRCA_CN_segments, # clust_method = "ward.D2", # plot_output= TRUE) ## ----PlotChrCluster_test, include=FALSE------------------------------------ Cluster <- PlotChrCluster(segs = test, clust_method = "ward.D2", plot_output= T) ## ----call output PlotChrCluster code, eval=FALSE--------------------------- # head(Cluster$report) # # #select plot table per sample # head(Cluster$plot_tables$`01428281-1653-4839-b5cf-167bc62eb147`) ## ----Call report PlotChrCluster 3------------------------------------------ knitr::kable(head(Cluster$report)) #select plot table per sample knitr::kable(head(Cluster$plot_tables$`01428281-1653-4839-b5cf-167bc62eb147`)) ## ----sessionInfo,echo=FALSE------------------------------------------------ sessionInfo()