Question: Calculate P-Value Of Ld Using Ldheatmap Package In R
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gravatar for 714
6.7 years ago by
71490
71490 wrote:

Does anyone know a way to calculate the p-values for the corresponding r2 and D' output of LDheatmap?

Thanks

R snp • 2.3k views
ADD COMMENTlink modified 6.5 years ago by Philipp Bayer6.7k • written 6.7 years ago by 71490
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gravatar for Philipp Bayer
6.5 years ago by
Philipp Bayer6.7k
Australia/Perth/UWA
Philipp Bayer6.7k wrote:

This is now a bit old, but I just saw it - the best way to get to the p-values is not to use LDHeatmap, but to use LD() of the "genetics" library. I don't think LDheatmap even has the capacity of giving you the p-values directly, the reference says nothing.

library(LDHeatmap)
# this is probably how you did it
genotypes <- read.csv("some_file")
LDheatmap(genotypes)

# this is easier
library(genetics)
results <- LD(genotypes)
head(results$p.value) # gives you the beginning of the p-values
head(results$D) # gives you the beginning of D
ADD COMMENTlink written 6.5 years ago by Philipp Bayer6.7k
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