coloc.process | R Documentation |
Internal helper function
coloc.process( obj, hits1 = NULL, hits2 = NULL, LD = NULL, r2thr = 0.01, p1 = 1e-04, p2 = 1e-04, p12 = 1e-06, LD1 = LD, LD2 = LD, mode = c("iterative", "allbutone") )
obj |
object returned by coloc.detail() |
hits1 |
lead snps for trait 1. If length > 1, will use masking |
hits2 |
lead snps for trait 2. If length > 1, will use masking |
LD |
named LD matrix (for masking) |
r2thr |
r2 threshold at which to mask |
p1 |
prior probability a SNP is associated with trait 1, default 1e-4 |
p2 |
prior probability a SNP is associated with trait 2, default 1e-4 |
p12 |
prior probability a SNP is associated with both traits, default 1e-5 |
LD1 |
named LD matrix (for masking) for trait 1 only |
LD2 |
named LD matrix (for masking) for trait 2 only |
mode |
either "iterative" (default) - successively condition on signals or "allbutone" - find all putative signals and condition on all but one of them in each analysis |
data.table of coloc results
Chris Wallace
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