Ld Plot For Imputed Dosage Data

Question

[zx8754]

We have imputed (impute2) data for a small region ~3000 snps. I know of Haploview that does LD plots for typed genotypes. Imputed data could be converted to exact genotype using plink with a threshold of, say 0.9, then use Haploview...

But I am wondering if there are any tools out there that would give me LD plots for imputed dosage data?

Sample data - it is a standard Impute2 output files. Here is example from gen file:

5    rs7727745    1212357    C    A    1    0    0    0    1    0
---    rs116469613    1212374    T    C    1    0    0    1    0    0
---    5-1212406    1212406    C    T    1    0    0    0.997    0.003    0
---    rs115871703    1212491    G    A    1    0    0    1    0    0
---    rs140343487    1212494    C    T    0.994    0.006    0    0.999    0.001    0
---    5-1212536    1212536    C    T    1    0    0    1    0    0

[Zev.Kronenberg]

Can you provide information as to the state of your data? Maybe a snippet?

[zx8754]

@Zev.Kronenberg sample data added to the question.

[potassiumiodide0990]

How did u plot the LD for the imputed data? I'm unable to in haploview

[zx8754]

I couldn't, I had to convert to genotypes with threshold at 0.9.

[potassiumiodide0990]

Can you please elaborate on that? How did you exactly convert the allelic dosage to genotype data?

Answer 1

[romsen]

Hi, I use the SNP.Plotter Package for R to generate LD Plots out from plink .ped files.

http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html

http://cran.r-project.org/web/packages/snp.plotter/