mJAM_LDpruning: Pruning SNPs based on LD

In USCbiostats/hJAM: Hierarchical Joint Analysis of Marginal Summary Statistics

Pruning SNPs based on LD

Description

Pruning SNPs based on LD

Usage

mJAM_LDpruning(target, testing, R, within_thre = 0.95, across_thre = 0.8)

Arguments

target	Target SNP ID.
testing	IDs of SNPs to be tested.
R	a list of correlation matrix of all SNPs.
within_thre	threshold of r2 with selected index SNP(s) within a single population. If a SNP's correlation with any selected index SNP is greater than this threshold in at least one population, it will be excluded from subsequent rounds of index SNP selection.
across_thre	threshold of r2 with selected index SNP(s) across all populations. If a SNP's correlation with any selected index SNP is greater than this threshold in all populations, it will be excluded from subsequent rounds of index SNP selection.

Value

remove_within

SNP IDs to be pruned due to high within-population correlation

remove_across

SNP IDs to be pruned due to high across-population correlation

Author(s)

Jiayi Shen

USCbiostats/hJAM documentation built on Jan. 26, 2024, 5:27 p.m.