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Dear Mike,
I am wondering How LD clumping was performed to select eQTLs for candidate gene in eQTL-based two-sample Mendelian Randomization? How to handle pleiotropy eQTL issue? for example, a SNP …
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Hi
I am having two dataset , as below
eqtl_fn
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Hello, I'm trying to use mashr to robustly compare my own eQTL results from three conditions.
Actually, I've already got three eQTL result sets from the condition-by-condition alaysis.
Those eQTL re…
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Hi, I applied this tool to a big public dataset and successfully got outcomes among several cell types.
My successful step1 command is like
Rscript /home/users/scratch/qtl/extdata/step1_fitNULLGLMM…
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Thanks for sharing such an excellent tool ! But I have problems that where or how to get **genome-wide eQTL summary statistics**(the example includes eQTL summary statistics for each gene), and how to…
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I am creating a single phenotype bed file from an eQTL list using CaVEMaN with the setting --single-signal. CaVEMaN is displaying the following error message:
376 individuals present in phenotype f…
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Thank you so much for your fast response to the previous issue. I am currently applying the GIFT_summary function on a real data example. The true causal gene should be gene4. The input for GIFT_summa…
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Hi! Thanks for the wonderful tool that your team developed! I was wondering if this method could be applied to scenarios outside eQTL where the matrix of effects is smaller (e.g. 1000 rows/tests in 10…
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List of remaining issues (also see https://centrepopgen.slack.com/archives/C018KFBCR1C/p1661145055698219?thread_ts=1658208231.938539&cid=C018KFBCR1C):
- [x] Drop alleles column
- [x] Merge `run_only…
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Hi there,
I have been trying to play around with the examples pre-installed with your package. However, I get a merge table error every time I try running the MR_MtRobin function? Can you please help…