Question: Is there any package for meta eqtl?
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gravatar for Fabrice Tourre
5.7 years ago by
Fabrice Tourre970 wrote:
Dear expert, I knew GGtools can do eqtl search. But I want a package to do meta eqtl. Because I cannot store all the output from the eqtl. I cannot do two eQTL separately, then combined them. Thank you very much in advance.
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ADD COMMENTlink modified 5.7 years ago by Vincent J. Carey, Jr.6.3k • written 5.7 years ago by Fabrice Tourre970
Answer: Is there any package for meta eqtl?
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gravatar for Vincent J. Carey, Jr.
5.7 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
if, by "meta eqtl" you mean metaanalysis of eqtl associations, a crude approach is available. given a set of smlSets from different populations, meqtlTests will harmonize the loci by name and compute the sum of association statistics across the populations. the ultimate results are of the same size as a single analysis. this particular approach has not gotten much mileage lately as we tend to do the separate analyses and combine later, now that we have sufficient disk. if you run into problems you can contact me directly. > args(meqtlTests) function (listOfSmls, rhslist, runname = "mfoo", targdir = "mfoo", geneApply = lapply, shortfac = 100, checkValid = TRUE, useUncertain = TRUE, glmfamily = "gaussian") NULL On Tue, Mar 18, 2014 at 2:16 PM, Fabrice Tourre <fabrice.ciup@gmail.com>wrote: > Dear expert, > > I knew GGtools can do eqtl search. But I want a package to do meta > eqtl. Because I cannot store all the output from the eqtl. I cannot do > two eQTL separately, then combined them. > > Thank you very much in advance. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.7 years ago by Vincent J. Carey, Jr.6.3k
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