## ----style-knitr, eval=TRUE, echo=FALSE, results='asis'-------------------- BiocStyle::latex() ## ----include=FALSE--------------------------------------------------------- library(knitr) opts_chunk$set( concordance=TRUE ) ## ----options, results='hide', message=FALSE, eval=TRUE, echo=FALSE---------------------- library(breakpointR) options(width=90) ## ----eval=FALSE------------------------------------------------------------------------- # library(breakpointR) # ## Run breakpointR with default paprameters # breakpointr(inputfolder='folder-with-BAMs', outputfolder='output-folder') ## ----eval=TRUE-------------------------------------------------------------------------- ?breakpointr ## ----eval=FALSE------------------------------------------------------------------------- # breakpointr(..., configfile='breakpointR.config') ## ----eval=FALSE------------------------------------------------------------------------- # callHotSpots=TRUE ## ----eval=TRUE, message=FALSE----------------------------------------------------------- library(breakpointR) ## Get some example files datafolder <- system.file("extdata", "example_bams", package="breakpointRdata") outputfolder <- tempdir() ## Run breakpointR breakpointr(inputfolder = datafolder, outputfolder = outputfolder, chromosomes = 'chr22', pairedEndReads = FALSE, reuse.existing.files = FALSE, windowsize = 1000000, binMethod = 'size', pair2frgm = FALSE, min.mapq = 10, filtAlt = TRUE) ## ----eval=FALSE------------------------------------------------------------------------- # breakpointr(..., min.mapq = 10, filtAlt = TRUE) ## ----eval=FALSE------------------------------------------------------------------------- # library(breakpointR) # ## Binning strategy based on desired bin length # breakpointr(inputfolder='folder-with-BAM', outputfolder='output-folder', # windowsize=1e6, binMethod='size') # ## Binning strategy based user-defined number of reads in each bin # breakpointr(inputfolder='folder-with-BAM', outputfolder='output-folder', # windowsize=100, binMethod='reads') ## ----eval=TRUE, warning=FALSE, message=FALSE-------------------------------------------- ## Example deltaW values exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata") exampleFile <- list.files(exampleFolder, full.names=TRUE)[1] breakpoint.object <- loadFromFiles(exampleFile) head(breakpoint.object[[1]]$deltas) ## ----eval=FALSE------------------------------------------------------------------------- # ## To run breakpoint hotspot analysis using the main breakpointR function # breakpointr(..., callHotSpots=TRUE) ## ----eval=TRUE, message=FALSE----------------------------------------------------------- ## To run breakpoint hotspot analysis using exported data exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata") exampleFiles <- list.files(exampleFolder, full.names=TRUE) breakpoint.objects <- loadFromFiles(exampleFiles) ## Extract breakpoint coordinates breaks <- lapply(breakpoint.objects, '[[', 'breaks') ## Get hotspot coordinates hotspots <- hotspotter(breaks, bw=1e6) ## ----eval=TRUE, warning=FALSE, message=FALSE, fig.width=12, fig.height=4---------------- ## Plotting a single library exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata") exampleFile <- list.files(exampleFolder, full.names=TRUE)[1] plotBreakpoints(exampleFile) ## ----eval=TRUE, warning=FALSE, message=FALSE, fig.width=12, fig.height=5---------------- ## Plotting a single library exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata") exampleFiles <- list.files(exampleFolder, full.names=TRUE)[1:4] plotBreakpointsPerChr(exampleFiles, chromosomes = 'chr7') ## ----sessionInfo, results='asis', eval=TRUE--------------------------------------------- toLatex(sessionInfo())