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CompositeLD

Build Status

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