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Question: Linkage disequilibrium with 1000 Genomes/HapMap
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gravatar for enricoferrero
3.3 years ago by
enricoferrero550
United Kingdom
enricoferrero550 wrote:
Hi, I have a set of SNPs associated with a specific trait and I would like to know to what other SNPs, in the 1000 Genomes [1] or HapMap [2] projects, they are in linkage disequilibrium (LD) with. Is there anything in Bioconductor (or CRAN) that can help me answer this question? I'm basically looking for something like SNAP Pairwise LD [3] from the Broad Institute. Thanks! [1] http://www.1000genomes.org/ [2] http://hapmap.ncbi.nlm.nih.gov/ [3] https://www.broadinstitute.org/mpg/snap/ldsearchpw.php -- Enrico Ferrero [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by enricoferrero550
1
gravatar for enricoferrero
3.3 years ago by
enricoferrero550
United Kingdom
enricoferrero550 wrote:
Hi, I have a set of SNPs associated with a specific trait and I would like to know to what other SNPs, in the 1000 Genomes [1] or HapMap [2] projects, they are in linkage disequilibrium (LD) with. Is there anything in Bioconductor (or CRAN) that can help me answer this question? I'm basically looking for something like SNAP Pairwise LD [3] from the Broad Institute. Thanks! [1] http://www.1000genomes.org/ [2] http://hapmap.ncbi.nlm.nih.gov/ [3] https://www.broadinstitute.org/mpg/snap/ldsearchpw.php -- Enrico Ferrero
ADD COMMENTlink written 3.3 years ago by enricoferrero550
Hi, You might want look at the trio package. http://www.bioconductor.org/packages/release/bioc/html/trio.html getLD() and getLDlarge() compute LD values genome-wide; findLDblocks() plots the LD matrix and estimates LD blocks. The functions can be applied to non-trio data by using the 'parentsOnly' argument. cc'ing the package author in case he has something else to add. Valerie On 07/21/2014 01:31 PM, Enrico Ferrero wrote: > Hi, > > I have a set of SNPs associated with a specific trait and I would like > to know to what other SNPs, in the 1000 Genomes [1] or HapMap [2] > projects, they are in linkage disequilibrium (LD) with. > > Is there anything in Bioconductor (or CRAN) that can help me answer > this question? I'm basically looking for something like SNAP Pairwise > LD [3] from the Broad Institute. > > Thanks! > > [1] http://www.1000genomes.org/ > [2] http://hapmap.ncbi.nlm.nih.gov/ > [3] https://www.broadinstitute.org/mpg/snap/ldsearchpw.php > -- Valerie Obenchain Program in Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, Seattle, WA 98109 Email: vobencha at fhcrc.org Phone: (206) 667-3158
ADD REPLYlink written 3.3 years ago by Valerie Obenchain ♦♦ 6.4k

Any R package that works "live" on 1000G data on the web without downloading?

ADD REPLYlink written 2.3 years ago by zx875410
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