top_snps_pval_ld2_new: Rank SNPs by pval, prune for LD
In jean997/sherlockAsh: CAUSE: Causal Analysis Using Summary Effect Estimates
Description
Selects a set of top SNP based on p-value that are in minimal LD.
Performs the same function as top_snps_pval_ld but with different input format.
Usage
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2
3
top_snps_pval_ld2_new(ld_files, snp_info_rds, snps, pval_cols = c(),
pval_thresh = Inf, r2_thresh = 0.01,
cores = parallel::detectCores() - 1)
Arguments
ld_files
List of h5 files containing pairwise ld. One for each chromosome.
snp_info_rds
RDS file with snp info
snps
List of snps
pval_thresh
Maximum pvalue
r2_thresh
r^2 threshold for pruning
cores
Number of cores to use
pvals
Vector of pvalues (optional)
jean997/sherlockAsh documentation built on May 18, 2019, 11:45 p.m.
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Description
Selects a set of top SNP based on p-value that are in minimal LD. Performs the same function as top_snps_pval_ld but with different input format.
Usage
1 2 3 | top_snps_pval_ld2_new(ld_files, snp_info_rds, snps, pval_cols = c(),
pval_thresh = Inf, r2_thresh = 0.01,
cores = parallel::detectCores() - 1)
|
Arguments
ld_files |
List of h5 files containing pairwise ld. One for each chromosome. |
snp_info_rds |
RDS file with snp info |
snps |
List of snps |
pval_thresh |
Maximum pvalue |
r2_thresh |
r^2 threshold for pruning |
cores |
Number of cores to use |
pvals |
Vector of pvalues (optional) |
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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