Question: Tool For Eqtl Mapping
gravatar for Paul
7.9 years ago by
United States
Paul750 wrote:

I have a significant SNP from a Genome Wide Association Study and I want to find correlation between change in this SNP between samples and change in gene expression.

I've manually used ANOVA in R which shows that many genes expression are associated with this SNP.

I'm wondering if there is another tool that anyone has used to perform this kind of analysis that would be staightforward to use. "Interval Mapping" seems to be the more accepted method for eQTL finding.

I've been trying to do this in GGtools but find the documentation to be limited which doesn't make life too easy.

eqtl • 5.2k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Paul750
gravatar for Peter Kang
7.3 years ago by
Peter Kang60
Peter Kang60 wrote:

Matrix eQTL seems to be a new R package for this purpose:

ADD COMMENTlink written 7.3 years ago by Peter Kang60
gravatar for David Quigley
7.9 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

Karl Broman (author of the very highly recommended R/QTL library) maintains a nice list of other software packages for QTL mapping on his RQTL web site. However, all of the software I'm familiar with is designed to do linkage analysis mapping loci in experimental genetic crosses (e.g. backcrosses or intercrosses with mice). When I have to map eQTL in human data, I've had to write my own scripts as you did using point mapping rather than the more informative interval mapping. A quick check of the Genetics view of bioconductor doesn't show anything obvious; there's a software gap here as far as I can tell.

The good news is that since you're a priori already interested in an exact locus, you have probably have already found the peak or near-peak of any interesting expression association with that locus in your dataset. The bad news is that you have a multiple testing problem; be sure to consider that when interpreting your results. It only gets worse if you consider all loci and all genes, though.

ADD COMMENTlink written 7.9 years ago by David Quigley11k
gravatar for Mary
7.9 years ago by
Boston MA area
Mary11k wrote:

Oh, I am so glad you asked this. At the last workshop I did someone asked me for tools for this, and I have been meaning to look for them.

I was going to investigate this one: Genevar But honestly I haven't yet, so I can't offer any guidance.

Looking forward to other answers.

ADD COMMENTlink written 7.9 years ago by Mary11k
gravatar for Khader Shameer
7.9 years ago by
Manhattan, NY
Khader Shameer17k wrote:

You can use SCANDB for scanning the SNP/regions for pre-computed eQTL. See the SNP and region tabs. I find it useful for a similar eQTL analysis. SCANDB manuscript is available here

ADD COMMENTlink written 7.9 years ago by Khader Shameer17k
gravatar for Rossella
7.9 years ago by
Rossella370 wrote:

You can use PLINK ( for performing association on quantitative traits. The software is quite powerful and straightforward. You just need to add expression as a quantitative phenotype in your input file.

ADD COMMENTlink written 7.9 years ago by Rossella370

But does PLINK actually perform interval mapping, which is what Paul is asking about? I'm not a PLINK expert but I think it only performs point estimation.

ADD REPLYlink written 7.9 years ago by David Quigley11k
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