Bayesian colocalisation analysis using snpStats objects

coloc.abf.snpStats(
  X1,
  X2,
  Y1,
  Y2,
  snps = intersect(colnames(X1), colnames(X2)),
  type1 = c("quant", "cc"),
  type2 = c("quant", "cc"),
  s1 = NA,
  s2 = NA,
  ...
)

Arguments

X1	genetic data for dataset 1
X2	genetic data for dataset 2
Y1	response for dataset 1
Y2	response for dataset 2
snps	optional subset of snps to use
type1	type of data in Y1, "quant" or "cc"
type2	type of data in Y2, "quant" or "cc"
s1	the proportion of samples in dataset 1 that are cases (only relevant for case control samples)
s2	the proportion of samples in dataset 2 that are cases (only relevant for case control samples)
...	parameters passed to `coloc.abf`

Value

output of coloc.abf

Details

Generates p values via score tests, then runs coloc.abf