## ----style, eval=TRUE, echo = FALSE, results = 'asis'---------------------- BiocStyle::latex() ## ----TCGA download, eval=FALSE--------------------------------------------- # BiocManager::install("TCGAbiolinks") # library(TCGAbiolinks) # # query <- GDCquery(project = "TCGA-BRCA", # data.category = "Copy Number Variation", # data.type = "Copy Number Segment", # sample.type = "Primary Tumor" # ) # # #Selecting first 100 samples using the TCGA barcode # subset <- query[[1]][[1]] # barcode <- subset$cases[1:100] # # TCGA_BRCA_CN_segments <- GDCquery(project = "TCGA-BRCA", # data.category = "Copy Number Variation", # data.type = "Copy Number Segment", # sample.type = "Primary Tumor", # barcode = barcode # ) # # GDCdownload(TCGA_BRCA_CN_segments, method = "api", files.per.chunk = 50) # # #prepare a data.frame where working # data <- GDCprepare(TCGA_BRCA_CN_segments, save = TRUE, # save.filename= "TCGA_BRCA_CN_segments.txt") # ## ----Column preparation, eval=FALSE---------------------------------------- # names(data) # BOBaFIT_names <- c("ID", "chr", "start", "end", "Num_Probes", # "Segment_Mean","Sample") # names(data)<- BOBaFIT_names # names(data) ## ----tcga load, include=FALSE---------------------------------------------- library(BOBaFIT) data("TCGA_BRCA_CN_segments") data <- TCGA_BRCA_CN_segments[1:9] ## ----Popeye, echo=TRUE, message=FALSE-------------------------------------- library(BOBaFIT) segments <- Popeye(data) ## ----Popeye table, echo=FALSE---------------------------------------------- knitr::kable(head(segments)) ## ----CN, echo=TRUE--------------------------------------------------------- #When data coming from SNParray platform are used, the user have to apply the #compression factor in the formula (0.55). In case of WGS/WES data, the #correction factor is equal to 1. compression_factor <- 0.55 segments$CN <- 2^(segments$Segment_Mean/compression_factor + 1) ## ----CN table, echo=FALSE-------------------------------------------------- knitr::kable(head(segments)) ## ----sessionInfo,echo=FALSE------------------------------------------------ sessionInfo()