genomewideLD: Genome-wide LD adjustment
In GMELab/GraBLD: Gradient Boosted and LD adjusted
Description
Usage
Arguments
Value
References
Description
The function compute the LD adjustment on the entire genotype data matrix by
first dividing them into SNP blocks.
Usage
1
genomewideLD(geno_data, size = 300)
Arguments
geno_data
the standardized genotype matrix assuming each row is the individual and each column is the SNP.
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 for all 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.
GMELab/GraBLD documentation built on May 4, 2019, 3:20 p.m.
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Description Usage Arguments Value References
Description
The function compute the LD adjustment on the entire genotype data matrix by first dividing them into SNP blocks.
Usage
1 | genomewideLD(geno_data, size = 300)
|
Arguments
geno_data |
the standardized genotype matrix assuming each row is the individual and each column is the SNP. |
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 for all 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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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