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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