cluster: Generate clusters of markers in high linkage disequilibrium

In malemay/HaplotypeMiner: Gene-centered haplotyping from SNP data

Generate clusters of markers in high linkage disequilibrium

Description

This function clusters groups of markers that are in high linkage disequilibrium on a single side of the central gene position considered. The objective of the clustering step is to reduce the number of markers considered and thus allow for a simplification of haplotype definition problem.

Usage

cluster(snp_data, center_pos, block_threshold = 1)

Arguments

snp_data	A list: the snp data to be clustered. Must contain at least Genotypes, LD and Markers fields for clustering to occur properly.
center_pos	The central position on either side of which clustering should be performed.
block_threshold	The minimum R^2 for two adjacent markers to be eligible for blocking (defaults to 1, i.e. perfect linkage disequilibrium).

Details

This function is used internally by the package and is not normally available for end users.

Value

A subset of the original snp_data containing only one representative marker per LD block.

Examples

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malemay/HaplotypeMiner documentation built on Feb. 6, 2024, 3:29 a.m.