Question: Estimating Ld Blocks
4
gravatar for Hanif Khalak
8.8 years ago by
Hanif Khalak1.2k
Doha, QA
Hanif Khalak1.2k wrote:

I'm trying to get a handle on how LD patterns define blocks which are often interpreted as haplotype boundaries. I have LD data (D', r^2) and would like to come up with or use an existing function which takes this matrix and can generate row IDs for the boundaries of each "block".

Is there a BioConductor package or other tool which does this, or a paper which describes a simple approach I could try? The matrix looks "block-diagonal" so I imagine even a technique from linear algebra might have a simple procedure, e.g. this Matlab function (which I don't have access to)?

linkage haplotype • 5.2k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 8.8 years ago by Hanif Khalak1.2k
3
gravatar for Khader Shameer
8.8 years ago by
Manhattan, NY
Khader Shameer18k wrote:

If you are can think out of R, you can try using PLINK (See section on LD calculations) or Haploview (See Haploview tutorial here) for estimation / visualization of LD blocks. I would like to recommend PLINK, it can be easily integrated in to your work-flows, but Haploview is more of a GUI based. If you are too specific on R, there is an R plug-in for PLINK too.

ADD COMMENTlink written 8.8 years ago by Khader Shameer18k

Thanks for the [p]link - I was hoping for something that I could use with the LD matrix and wouldn't require the raw genotypes

ADD REPLYlink written 8.8 years ago by Hanif Khalak1.2k
2
gravatar for Laurent Gautier
8.7 years ago by
Laurent Gautier810 wrote:

LDheatmap (although on CRAN, not on Bioconductor) will help with making a visualization of your LD data. The function retuns (invisibly) an object with details for the plot that you could use.

For dealing with almost-block matrices, the packges limSolve might have utilities.

ADD COMMENTlink written 8.7 years ago by Laurent Gautier810
2
gravatar for Larry_Parnell
8.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

We do a lot of this in our group and I mean a lot. Our choices are HelixTree (GoldenHelix) and TAGGER/Haploview (Haploview employs TAGGER). I have heard a lot of talk about PLINK. Our collaborators with the GOLDN study use it. We find HelixTree to be more robust.

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Larry_Parnell16k
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