Question: Ld Plot For Imputed Dosage Data
0
gravatar for zx8754
7.3 years ago by
zx87547.8k
London
zx87547.8k wrote:

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
ld • 2.8k views
ADD COMMENTlink modified 6.1 years ago by romsen60 • written 7.3 years ago by zx87547.8k

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

ADD REPLYlink written 7.3 years ago by Zev.Kronenberg11k
1

@Zev.Kronenberg sample data added to the question.

ADD REPLYlink written 7.3 years ago by zx87547.8k

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

ADD REPLYlink written 5.0 years ago by potassiumiodide099080

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

ADD REPLYlink written 5.0 years ago by zx87547.8k

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

ADD REPLYlink written 5.0 years ago by potassiumiodide099080
0
gravatar for romsen
6.1 years ago by
romsen60
romsen60 wrote:

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/

ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by romsen60
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