README.Rmd

---
title: "Big-LD: A new haplotype block detection method"
author: "Sunah Kim (sunny03@snu.ac.kr)"
output: rmarkdown::github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r, echo = FALSE}
knitr::opts_chunk$set(
  fig.path = "README_figs/README-"
)
```

# Big-LD

Big-LD is a block partition method based on interval graph modeling of LD bins which are clusters of strong pairwise LD SNPs, not necessarily physically consecutive.
The detailed information about the Big-LD can be found in our paper published in [bioinformatics](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx609/4282661/A-new-haplotype-block-detection-method-for-dense).

The Big-LD algorithm and visualization function has been updated and implemented in a new package "gpart". 
The package "gpart" can be downloaded from [bioconductor](https://bioconductor.org/packages/devel/bioc/html/gpart.html)

The "gpart" has following features.

### the updated `BigLD` function
* supports two types of heuristic algorithm, `near-nonhrst` and `fast`. 
* supports LD measures r2 and D' both.
* supports PLINK formats (.ped, .map, .raw, .traw) and vcf format as input

### the updated `LDblockHeatmap` function
* shows up to 20000 SNPs.
* shows physical locations of LD blocks and SNPs
* shows gene locations if the gene information is inputted (or by loading gene information from the Ensembl or UCSC database) .

### the new SNP sequence partition algorithm `GPART`
* divides the entire SNP sequence using LD block information (BigLD result) and gene information
* can limit the min/max size of a block


### A BigLD result plotted by the updated `LDblockHeatmap()` in "gpart" package. 

* EAS population of 1000 Genomes phase 1 data
* chr1:16Mb-17.9Mb  
```{r, out.width = "1200px", echo = FALSE}
knitr::include_graphics("README_figs/README-heatmap_all.png")
```