Question: How to put a line of LD-decay in a LD vs distance plot?
1
gravatar for vyoouh
6.0 years ago by
vyoouh20
France
vyoouh20 wrote:

Hi guys, 

I am now working to create a LD vs distance plot in R using an output from PLINK which contain seven columns:

CHR_A, BP_A, SNP_A, CHR_B, BP_B, SNP_B, R2.  Then I subtract the value of  BP_B and BP_A, plot it with R2 value. The graph looks nice, however, I want my graph to have an average line like an example of FIGURE5 in here http://www.hutton.ac.uk/webfm_send/546. How can I add in the line, what should be a code in R for that?

thanks,

J.

ld • 7.9k views
ADD COMMENTlink modified 6.0 years ago by Fabio Marroni2.5k • written 6.0 years ago by vyoouh20
1
gravatar for Fabio Marroni
6.0 years ago by
Fabio Marroni2.5k
Italy
Fabio Marroni2.5k wrote:

Hi, 

I wrote a blog post on this, you might want to give a look.

http://fabiomarroni.wordpress.com/2011/08/09/estimate-decay-of-linkage-disequilibrium-with-distance/

There are two versions, one using R2 and one using D'.

Hope this helps!

 

ADD COMMENTlink written 6.0 years ago by Fabio Marroni2.5k
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