View source: R/genomic_statistics.R
adjLD | R Documentation |
Perform LD pruning of summary statistics before they are used in gene set enrichment analyses.
adjLD(
stat = NULL,
Glist = NULL,
chr = NULL,
statistics = "p-value",
r2 = 0.9,
ldSets = NULL,
threshold = 1,
method = "pruning"
)
stat |
A data frame with marker summary statistics. Ensure that it is in the correct format. |
Glist |
List of information about the genotype matrix stored on disk. |
chr |
Chromosome(s) being processed. |
statistics |
Specify what type of statistics ("b", "z", or "p-value") is being processed. Default is "p-value". |
r2 |
Threshold used in the clumping/pruning procedure. Default is 0.9. |
ldSets |
List of marker sets - names correspond to row names in 'stat'. |
threshold |
P-value threshold used in LD pruning. |
method |
Method used in adjustment for linkage disequilibrium. Options are "pruning" or "clumping". Default is "pruning". |
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