## ----style, eval=TRUE, echo=FALSE, results="asis"-------------------------- BiocStyle::latex() ## ----echo=FALSE, results='hide'-------------------------------- set.seed(1) options(width=65) library(knitr) opts_chunk$set(background = "#FFFFFF", comment = NA, fig.path = "") ## ----load_packages,results='hide'------------------------------ library(VariantAnnotation) library(GenomicRanges) ## ----load_data------------------------------------------------- data(package = "COSMIC.67") data(cosmic_67, package = "COSMIC.67") ## ----overlap_with_tp53----------------------------------------- tp53_range = GRanges("17", IRanges(7565097, 7590856)) vcf_path = system.file("vcf", "cosmic_67.vcf.gz", package = "COSMIC.67") cosmic_tp53 = readVcf(vcf_path, genome = "GRCh37", ScanVcfParam(which = tp53_range)) cosmic_tp53 ## ----CGC------------------------------------------------------- data(cgc_67, package = "COSMIC.67") head(cgc_67) ## ----echo=FALSE------------------------------------------------ sessionInfo()