## ----setup, include=FALSE------------------------------------------------ suppressMessages(library(GenomicRanges)) library(knitr) knitr::opts_chunk$set(echo = TRUE) opts_knit$set(root.dir = system.file("extdata", package = "RepViz")) ## ----download BAM,eval = FALSE------------------------------------------- # file.copy(from = list.files(system.file("extdata", package = "RepViz"), full.names = TRUE),to = tempdir()) # setwd(tempdir()) ## ----input BAM, echo=FALSE----------------------------------------------- BAM_table <- read.table(system.file("extdata","BAM_input.csv", package = "RepViz"), sep = ",") colnames(BAM_table) <- c("bam file","group") knitr::kable(BAM_table) ## ----input BED, echo=FALSE----------------------------------------------- BED_table <- read.table(system.file("extdata","BED_input.csv", package = "RepViz"), sep = ",") colnames(BED_table) <- c("bed file","Legend") knitr::kable(BED_table) ## ----bam files, echo=FALSE----------------------------------------------- list.files(system.file("extdata", package = "RepViz"),pattern = ".bam") ## ----plot_code,fig.height=10,fig.width=7,prompt=FALSE,eval = FALSE------- # region <- GRanges("chr12:110938000-110940000") # RepViz::RepViz(region = region, # genome = "hg19", # BAM = "BAM_input.csv", # BED = "BED_input.csv", # avgTrack = TRUE, # geneTrack = TRUE, # verbose = FALSE) # # # ## ----plot_plot,fig.height=10,fig.width=7,prompt=FALSE, echo=FALSE-------- region <- GRanges("chr12:110938000-110940000") RepViz::RepViz(region = region, genome = "hg19", BAM = "BAM_input.csv", BED = "BED_input.csv", avgTrack = TRUE, geneTrack = TRUE, verbose = FALSE)