## ----libraryLoad--------------------------------------------------------- suppressMessages(library(metagene)) ## ----bamFiles------------------------------------------------------------ bam_files <- get_demo_bam_files() bam_files ## ----regionsArgument----------------------------------------------------- regions <- get_demo_regions() regions ## ----designFile---------------------------------------------------------- fileDesign <- system.file("extdata/design.txt", package="metagene") design <- read.table(fileDesign, header=TRUE, stringsAsFactors=FALSE) design$Samples <- paste(system.file("extdata", package="metagene"), design$Samples, sep="/") design ## ----alternateDesign----------------------------------------------------- design <- data.frame(Samples = c("align1_rep1.bam", "align1_rep2.bam", "align2_rep1.bam", "align2_rep2.bam", "ctrl.bam"), align1 = c(1,1,0,0,2), align2 = c(0,0,1,1,2)) design$Samples <- paste0(system.file("extdata", package="metagene"), "/", design$Samples) design ## ----initializeMetageneObj----------------------------------------------- mg <- metagene$new(regions, bam_files) ## ----producePlotEx1------------------------------------------------------ results <- mg$plot(range = c(-1000,1000)) ## ----showDataFrame, collapse=TRUE---------------------------------------- class(results) names(results) head(results$DF)