cluster_selection: Selecting marker clusters according to filtering criteria

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

Selecting marker clusters according to filtering criteria

Description

This function selects marker clusters to be used for haplotype generation. Clusters are selecte based on three different analysis criteria : high enough linkage disequilibrium between marker pairs (parameter ld_threshold), proximity between markers in a pair (parameter max_pair_distance), and proximity between markers and gene center position (parameter max_marker_distance).

Usage

cluster_selection(snp_data, center_pos, ld_threshold = 0.5,
  max_pair_distance = 10^10, max_marker_distance = 10^10)

Arguments

snp_data	A list describing snp_data and containing at least two items : Markers A data.frame containing metadata regarding the markers to be selected, as output by functions read_hapmap and read_vcf . LD A square matrix containing linkage disequilibrum measures (could be either R2, R2v, R2s or R2vs) between all gene pairs.
center_pos	A numeric of length one. The central position of the gene of interest.
ld_threshold	A numeric between 0 and 1. The minimum LD value to pass the filter. Defaults to 0.5.
max_pair_distance	A numeric of length one. The maximum distance (in base pairs) between two markers in a pair for markers in that pair to be selected.
max_marker_distance	A numeric of length one. The maximum distance (in base pairs) between the marker and the gene center for a marker to be selected.

Details

This function is meant for internal package use only. It is called by function haplo_selection in the final stage of marker selection.

Value

A list similar to that provided as input, but with a subset of markers that passed the filters.

Examples

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