plinkLD: The LD info from output of the software (plink)
In SummaryLasso: Building Polygenic Risk Score Using GWAS Summary Statistics
Description
Usage
Format
References
Description
The LD information is crucial for the analysis by SummaryLasso.
The reference alleles used to obtained for the Z statsitics or the
regression coefficients have to be the sames as those used for the LD calculation.
This file can be obtained directly from the output of the LD calculation by the
software (plink); for example the output can be like plink.ld.
On the other hand, the user can calcuate the LD based on their prefered tools.
The variables are as
follows:
CHR_A: The chromosome of SNP_A
BP_A: The positions of SNP_A
SNP_A: The names of SNP_A
CHR_B: The chromosome of SNP_B
BP_B: The positions of SNP_B
SNP_B: The names of SNP_B
R: The correlation between SNP_A and SNP_B
Usage
1
Format
A data frame with 205959 rows and 7 columns
References
Purcell S, et al. (2007)
PLINK: a toolset for whole-genome association and population-based
linkage analysis. American Journal of Human Genetics, 81.
SummaryLasso documentation built on Nov. 15, 2019, 5:10 p.m.
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Description Usage Format References
Description
The LD information is crucial for the analysis by SummaryLasso. The reference alleles used to obtained for the Z statsitics or the regression coefficients have to be the sames as those used for the LD calculation. This file can be obtained directly from the output of the LD calculation by the software (plink); for example the output can be like plink.ld. On the other hand, the user can calcuate the LD based on their prefered tools. The variables are as follows:
CHR_A: The chromosome of SNP_A
BP_A: The positions of SNP_A
SNP_A: The names of SNP_A
CHR_B: The chromosome of SNP_B
BP_B: The positions of SNP_B
SNP_B: The names of SNP_B
R: The correlation between SNP_A and SNP_B
Usage
1 |
Format
A data frame with 205959 rows and 7 columns
References
Purcell S, et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.
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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