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        "description": "## ld_estimator: A package to estimate linkage disequilibrium\nComputes linkage disequilibrium in python. This uses the maximum-likelihood of\n[Excoffier & Slatkin](https://doi.org/10.1093/oxfordjournals.molbev.a040269),\njust converted from [HaploView](https://github.com/jazzywhit/Haploview) to c++\n, with python bindings. It's not too slow, can calculate ~1000 pairs per\nsecond.\n\n### Installation\nThe simplest way to install ld_estimator is through pip:\n```sh\npip install ld_estimator\n```\n\n### Usage\nUse ld_estimator within a python environment\n```python\nfrom ld_estimator import pairwise_ld\n\nvar1 = [(0, 0), (0, 0), (0, 1), (1, 0), (1, 1), (0, 1), (0, 0), (0, 0), (1, 1)]\nvar2 = [(0, 0), (0, 0), (0, 1), (1, 0), (1, 1), (0, 1), (0, 0), (1, 1), (1, 1)]\nis_haploid = [False, False, False, False, False, False, False, True, True, True]\nld = pairwise_ld(var1, var2, is_haploid)\nprint(ld.dprime)\nprint(ld.r_squared)\n\n# or calculate LD for all pairs of variants in a region in a VCF:\nfrom ld_estimator import region_ld\nvcf_path = 'PATH_TO_VCF'\nld = region_ld(vcf_path, chrom, start, end)\n\n# or calculate LD to a site within a region in a VCF. This defaults to checking\n# variants within a 100 kb window of the specified site.\nfrom ld_estimator import site_ld\nvcf_path = 'PATH_TO_VCF'\nld = site_ld(vcf_path, chrom, pos, window=200000)\n\n# can pass in multiple positions in the same region at once\nld = site_ld(vcf_path, chrom, [pos2, pos2, pos3], window=200000)\n\n# both region_ld() and site_ld() can take a list of sample IDs to subset the\n# samples used for calculating LD. For example:\nld = site_ld(vcf_path, chrom, pos, subset=['sample1', 'sample2'])\n\n# if the variant is on a sex chromosome, you'll have to pass in a list of sample\n# sexes (matching order of the subset IDs if present, otherwise the VCF samples)\nld = site_ld(vcf_path, 'X', 20000000, sexes=['male', 'female'])\n```",
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