regionalLD: Regional LD adjustment

In GMELab/GraBLD: Gradient Boosted and LD adjusted

Description

The function calculates the LD adjustment of each SNP for one given size of genotype data block.

Usage

regionalLD(geno_data, position = "start", size = 300)

Arguments

geno_data	the standardized genotype matrix assuming each row is the individual and each column is the SNP.
position	a character indicating the position of the SNP in a block of SNPs, one of start (the start of the block), mid (the middle of the block), end (the end of the block), or together (combining SNPs in a few blocks), short (in a short block), or all (using all regions).
size	an integer for the number of SNPs that should be included in a block. Usually, for genome-wide datasets, there are about 2 million SNPs and +/- 300 SNPs is roughly equivalent to 1Mb physical distance, thus 300 is set as the default size.

Value

a numeric vector of LD adjustments with the same length as the number of SNPs in the genotype matrix.

References

Pare, Guillaume, Shihong Mao, and Wei Q. Deng. A method to estimate the contribution of regional genetic associations to complex traits from summary association statistics. Scientific reports 6 (2016): 27644.

Examples

data(geno)
norm_geno <- full_normal_geno(geno_raw = geno)
regLD <- regionalLD(geno_data = norm_geno, position = 'mid', size = 300)
print(regLD)

GMELab/GraBLD documentation built on May 4, 2019, 3:20 p.m.