inst/doc/a03_enumeration.R

In coloc: Colocalisation Tests of Two Genetic Traits

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library(coloc)
data(coloc_test_data)
attach(coloc_test_data)

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plot_dataset(D1)
my.res <- finemap.abf(dataset=D1)
my.res[21:30,]

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my.res <- coloc.abf(dataset1=D1,
                    dataset2=D2)
print(my.res) 

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subset(my.res$results,SNP.PP.H4>0.01)

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o <- order(my.res$results$SNP.PP.H4,decreasing=TRUE)
cs <- cumsum(my.res$results$SNP.PP.H4[o])
w <- which(cs > 0.95)[1]
my.res$results[o,][1:w,]$snp