Skip to content

Latest commit

 

History

History
35 lines (23 loc) · 1.64 KB

README.md

File metadata and controls

35 lines (23 loc) · 1.64 KB
Raw

Big-LD: A new haplotype block detection method

Sunah Kim ([email protected])

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.

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

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