knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
The goal of fragCounter is to correct Whole genome or targeted sequencing data for GC and mappability bias. The GC bias curve is determined by loess regression of read count by GC and mappability scores. Segmentation is done by circular binary segmentation (CBS) algorithm after getting tumor/normal ratios of corrected read counts.
You can install fragCounter from github with:
Install dependent packages
install.packages('DNAcopy')
Install devtools from CRAN (if you don't have it already)
install.packages('devtools')
Install dependent mskilab R packages
devtools::install_github('mskilab/gUtils')
Install fragCounter
devtools::install_github("mskilab/fragCounter")
This is a basic example which shows you how to solve a common problem:
## basic example code
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