Dataset Information

Crosshap: R package for local haplotype visualization for trait association analysis.

ABSTRACT:

Summary

Genome-wide association studies (GWAS) excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present crosshap, an R package that performs robust density-based clustering of variants based on their linkage profiles to capture haplotype structures in a local genomic region of interest. Following this, crosshap is equipped with visualization tools for choosing optimal clustering parameters (ɛ) before producing an intuitive figure that provides an overview of the complex relationships between linked variants, haplotype combinations, phenotype, and metadata traits.

Availability and implementation

The crosshap package is freely available under the MIT license and can be downloaded directly from CRAN with R >4.0.0. The development version is available on GitHub alongside issue support (https://github.com/jacobimarsh/crosshap). Tutorial vignettes and documentation are available (https://jacobimarsh.github.io/crosshap/).

SUBMITTER: Marsh JI

PROVIDER: S-EPMC10471896 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Publications

crosshap: R package for local haplotype visualization for trait association analysis.

Marsh Jacob I JI Petereit Jakob J Johnston Brady A BA Bayer Philipp E PE Tay Fernandez Cassandria G CG Al-Mamun Hawlader A HA Batley Jacqueline J Edwards David D

Bioinformatics (Oxford, England) 20230801 8

<h4>Summary</h4>Genome-wide association studies (GWAS) excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present crosshap, an R package that performs robust density-based clustering of variants based on their linkage profiles to capture ...[more]

PMID: 37607004

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