## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( tidy.opts = list(width.cutoff=100), tidy = FALSE, message = FALSE, collapse = TRUE, comment = "#>" ) ## ----pull_DNAfusion, message=FALSE, results = 'hide', echo = FALSE------------ library(DNAfusion) ## ----setup_bioconductor, message=FALSE, results = 'hide', eval = FALSE-------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("DNAfusion") # library(DNAfusion) # ## ----examples----------------------------------------------------------------- H3122_bam <- system.file("extdata", "H3122_EML4.bam", package = "DNAfusion") HCC827_bam <- system.file("extdata", "HCC827_EML4.bam", package = "DNAfusion") ## ----EML4_ALK_detection2------------------------------------------------------ H3122_result <- EML4_ALK_detection(file = H3122_bam, genome = "hg38", mates = 2) head(H3122_result) ## ----EML4_ALK_detection3------------------------------------------------------ HCC827_result <- EML4_ALK_detection(file = HCC827_bam, genome = "hg38", mates = 2) HCC827_result ## ----EML4_sequence------------------------------------------------------------ EML4_sequence(H3122_result, genome = "hg38", basepairs = 20) EML4_sequence(HCC827_result, genome = "hg38", basepairs = 20) ## ----ALK_sequence------------------------------------------------------------- ALK_sequence(H3122_result, genome = "hg38", basepairs = 20) ALK_sequence(HCC827_result, genome = "hg38", basepairs = 20) ## ----break_position----------------------------------------------------------- break_position(H3122_result, genome = "hg38", gene = "EML4") break_position(HCC827_result, genome = "hg38", gene = "EML4") ## ----break_position_depth----------------------------------------------------- break_position_depth(H3122_bam, H3122_result, genome = "hg38", gene = "EML4") break_position_depth(HCC827_bam, HCC827_result, genome = "hg38", gene = "EML4") ## ----EML4_ALK_analysis_results, message=FALSE--------------------------------- H3122_results <- EML4_ALK_analysis(file = H3122_bam, genome = "hg38", mates = 2, basepairs = 20) HCC827_results <- EML4_ALK_analysis(file = HCC827_bam, genome = "hg38", mates = 2, basepairs = 20) ## ----EML4_ALK_analysis_output1------------------------------------------------ head(H3122_results$clipped_reads) ## ----EML4_ALK_analysis_output2------------------------------------------------ H3122_results$last_EML4 H3122_results$first_ALK H3122_results$breakpoint_ALK H3122_results$breakpoint_EML4 H3122_results$read_depth_ALK H3122_results$read_depth_EML4 HCC827_results ## ----introns_ALK_EML4_results, message=FALSE---------------------------------- introns_ALK_EML4(file=H3122_bam,genome="hg38") introns_ALK_EML4(file=HCC827_bam,genome="hg38") ## ----ifind_variants_results, message=FALSE------------------------------------ find_variants(file=H3122_bam,genome="hg38") find_variants(file=HCC827_bam,genome="hg38") ## ----session, echo = FALSE---------------------------------------------------- sessioninfo::session_info( pkgs = "attached", include_base = FALSE, dependencies = NA, to_file = FALSE )