README.md

In Yin1012/BreakViz: R Package Template

BreakViz

Overview

The goal of BreakViz is to detect possible breakpoints' location in human whole genome sequencing data from MinION and visualize them with by using heatmap.

After sequencing and mapping, human DNA will be transformed into a bed file.The bed format file will be used as import in my package. User must provides two filters about selecting breakpoints : MinOverlap, Maxdistance. We will select possible breakpoints based on these two parameters and create a heat table for whole reads. The package will add heat to reads based on their status after filtering. After visulization, a heatmap version of chromosomes will be showed.

Dependencies

chromoMap, shiny

Installation

You can install BreakViz from github with:

devtools::install_github("Yin1012/BreakViz")

Example pipeline

This is a basic example which shows you how to solve a common problem:

#prepare work
library(devtools)
BiocManager::install("rtracklayer")
library(rtracklayer)
devtools::load_all(".")

#import bedfile
bedFile <- import(system.file("extdata", "test_file_4.bed", package = "BreakViz"), format = "bed")

#visualize the possible pairs
visPossiblePair(bedFile, minOverlap = 100, maxDistance = 1000, baseCol = 1)

#run shiny app
runApp('R/BreakVizApp.R')

Sample output

Yin1012/BreakViz documentation built on May 14, 2019, 4:01 a.m.