charge_top_hits_cleaned: GWAS top hits for arachidonic acid in the CHARGE consortium...
In MRCIEU/mrQC: CheckSumStats
charge_top_hits_cleaned R Documentation
GWAS top hits for arachidonic acid in the CHARGE consortium after post-GWAS cleaning
Description
The dataset contains rsids for single nucleotide polymorphisms extracted from a genome-wide association study of arachidonic acid in the CHARGE consortium. Prior to extraction of the rsids, SNPs were excluded if they had a minor allele frequency <=5%, an imputation r2 score <=0.5 or were present in only 1 study (out of a total of 5 studies in the meta-analysis). This filtering steps are based on the post-GWAS filtering steps described in Guan et al (PMID=24823311). The list of rsids was then generated by: 1) extracting all SNPs with P values <5e-8 (219 SNPs in total); and then 2) performing LD clumping on the 219 extracted SNPs (clump_r2 = 0.01, clump_kb=10000 ) using European participants from UK Biobank as a reference dataset (6 SNPs remained after LD clumping). Clumping was performed using ieugwasr::ld_clump.
Usage
charge_top_hits_cleaned
Format
A charactor vector of length 6:
Source
MRCIEU/mrQC documentation built on May 6, 2023, 1:40 p.m.
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| charge_top_hits_cleaned | R Documentation |
GWAS top hits for arachidonic acid in the CHARGE consortium after post-GWAS cleaning
Description
The dataset contains rsids for single nucleotide polymorphisms extracted from a genome-wide association study of arachidonic acid in the CHARGE consortium. Prior to extraction of the rsids, SNPs were excluded if they had a minor allele frequency <=5%, an imputation r2 score <=0.5 or were present in only 1 study (out of a total of 5 studies in the meta-analysis). This filtering steps are based on the post-GWAS filtering steps described in Guan et al (PMID=24823311). The list of rsids was then generated by: 1) extracting all SNPs with P values <5e-8 (219 SNPs in total); and then 2) performing LD clumping on the 219 extracted SNPs (clump_r2 = 0.01, clump_kb=10000 ) using European participants from UK Biobank as a reference dataset (6 SNPs remained after LD clumping). Clumping was performed using ieugwasr::ld_clump.
Usage
charge_top_hits_cleaned
Format
A charactor vector of length 6:
Source
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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