Bayesian colocalisation analysis using snpStats objects

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Description

Bayesian colocalisation analysis using snpStats objects

Usage

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  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

Details

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

Value

output of coloc.abf

Author(s)

Chris Wallace