eQTL analysis considering P-values
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3.9 years ago

Is there any eQTL analysis tool or an R package out there that considers P-value for analysis?

eQTL SNP R genome • 2.5k views
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3.9 years ago

For generic QTL analyses, I'd recommend the MatrixEQTL package and associated methodology. It's blazing fast providing you have the right LINPACK libraries.

Website / Paper / Package (CRAN)

Check out the website for some useful examples and configurations

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Yes i can confirm, I also highly recommend Matrix eQTL, it is extremely fast and you can add covariates if any in your experimental design.

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Thank you both. I hope you're suggesting me this after having a look at the above mentioned dataset.

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I believe that the above mentioned dataset is a result of a certain experiment. Does anybody concur? It does say so that there were 15 cohorts involved. So my question is, is this something like WGS (Whole Genome Sequencing)? Forgive me if this a very basic question since I'm fairly new to this. Thanks.

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make a screenshot of the dataset and I can tell you more. I am not in the condition now to download 63.3 Mb of a file.

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you have a table that might be the output of a tool that is performing such eQTL or QTL analysis, so please formulate again your question. What do you want to know?

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Can I use P value as a factor for identifying significant SNPs?

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you can select cut-off threshold to work with significant SNP. The cut-off threshold should be selected according to sample size to avoid false positive results. A P.val <= 0.01 is a good start but again, select a cut off for eQTL or GWAS or QTL depends on the number of SNPs that you are testing and how many people you used for the test...

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Hi Andrew, I am wondering how many eQTL from GTEx are solid and credible? 10%, 50% or 70%? Is there any way to design a study to validate and evaluate it?

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3.9 years ago
EagleEye 7.3k

While I was reading about eQTL studies I came across this tool called METASOFT. Since you did not provide much information in your post, I do not know how relevant this tool will be for your analysis.

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Thanks EagleEye. Basically I wanted to analyse data contained in this link :- https://www.niagads.org/igap-summary-statistics-adgc-only. Any thoughts?

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I believe that the above mentioned dataset is a result of a certain experiment. Does anybody concur? It does say so that there were 15 cohorts involved. So my question is, is this something like WGS (Whole Genome Sequencing)? Forgive me if this a very basic question since I'm fairly new to this. Thanks.

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Also, could you please brief me out the difference between identifying DEGs (Differentially Expressed Genes) and eQTLs.

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In simple terms as I understood,


Differential expression analysis: Finding difference in expression between two groups/tissues.

eQTL: Association of SNPs/polymorphisms with expression in specific/different tissues OR finding the effect of SNPs/polymorphisms on expression in specific/multiple tissues


Personally so far, I did not get a chance to handle eQTL dataset. Since the information looks fascinating, I just started reading about it. You can have a look at these articles related to eQTL studies from the following link.

A: How to integrate GTEx data for variant annotation to understand the tissue speci

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Will check it out. Kindly update if you figure out how to process the above mentioned dataset. Thanks again.

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3.5 years ago
juhuvn • 0

Is there any one give a try on eQTL analysis pipeline from molgenis? Here is the link: https://github.com/molgenis/systemsgenetics/wiki/eQTL-mapping-analysis-cookbook-(eQTLGen)#step-1---preparation-of-expression-data

How does it compare to matrixQTL?

And, what is covariate file? I cant find its definition/explanation anywhere.

Thank you

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