## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) library('tLOH') library('purrr') library('dplyr') library('GenomicRanges') library('VariantAnnotation') ## ----dataImport, eval=FALSE, warnings = FALSE--------------------------------- # exampleData <- tLOHDataImport('../inst/extdata/Example.vcf') # # The VCF file in inst/extdata must be decompressed before running this command ## ----marginalCalculations, eval=TRUE------------------------------------------ load("../data/humanGBMsampleAC.rda") df <- tLOHCalc(humanGBMsampleAC) head(df) ## ----plotting, eval=TRUE------------------------------------------------------ alleleFrequencyPlot(df, "Example") aggregateCHRPlot(df, "Example")