CompositeLD

This repository is under developpement, any suggestion is welcome! 😃

Overview

CompositeLD is a package using SnpArrays to perform some usefull calculations related LD. In particular :

• Calculate LD between two SNPs (given position or id in PLINK files)
• Get the LD matrix of a group of SNPs
• Get Strongly correlated SNPs to a given group of SNPs
• Clumping given SNPs in a prioritized order.

Example

using SnpArrays
using CompositeLD

data = SnpData(SnpArrays.datadir(datapath))

ld = ld_r2("rs1234", "rs654321", data)

ld_mat = getLDmat(data, [(1, 459876), (1, 58735), (2, 97654)])

strong = getStrongLD(data, ["rs1234", "rs5678"])

kept_v_b = clump(data, [(1, 459876), (1, 58735), (2, 97654)])

TO DO

• Better documentation
• Implementation of various LDLink/PLINK functionalities
  • LD matrix all snps in window
  • Visualise LD in a locus
  • PGEN format support + happlotypes
  • Covariance, LD with happlotypes