Question: Plotting LD decay in window
gravatar for Adrian Pelin
6.6 years ago by
Adrian Pelin2.4k
Adrian Pelin2.4k wrote:


I am trying to plot LD decay with a sliding window in R. What I want to have on my X axis is distance between 2 SNPs while my Y axis can have the mean r^2 value.

So far this is what I have:


# Find distances between pairs of SNPs
dist18 <- (a18[,2] - a18[,1])

# Store r^2 and distances in a zoo matrix

D18 <- zoo(a18[,13], dist18)

plot(rollapply(D18, width = 10, by = 1, FUN = mean, align = "left"), main="r^2 along genome, window of 10", ylab="r^2 (MLE)", xlab="Genome Position (bp)")

My insert sizes for my reads are not longer than 300bp, so I can only plot up to 300bp. For something like that, a window size of 10 sliding by 1 should eliminate a lot of noise and show how the mean changes. What ends up happening however is this:

1 1 1 1 1 1
0 0 0 0 0 0
Warning message:
In zoo(rval[i], index(x)[i]) :
  some methods for \u201czoo\u201d objects do not work if the index entries in \\u2019 are not unique

Indeed, the values are not unique, and there are many values for a distance of 1bp, 2bp... so when I plot a sliding window, it is not a sliding window of basepairs, but rather of values in the vector (the first 10 values of r^2 all correspond to a distance of 1bp).

This causes the plot to still be noise, even with windows of 50.

My question is, how can I get an average of all values of r^2 for distance of 1bp, then average for 2bp... store that in a vector, then plot?

Thank you.



plot ld r^2 R • 3.6k views
ADD COMMENTlink modified 6.6 years ago by Zev.Kronenberg11k • written 6.6 years ago by Adrian Pelin2.4k
gravatar for Zev.Kronenberg
6.6 years ago by
United States
Zev.Kronenberg11k wrote:

I wrote a tool that provides the average D across a window.  Works directly from a VCF file.

ADD COMMENTlink written 6.6 years ago by Zev.Kronenberg11k

Hello, your tool requires phased VCF data. I am not sure how to phase my data, since I am working on non-models.

ADD REPLYlink written 6.6 years ago by Adrian Pelin2.4k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 926 users visited in the last hour