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hakyimlab / PredictDB-Tutorial

Tutorial for running the PredictDB pipeline with GEUVADIS data
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How to set SNP window from gene TSS? #7

Open fernandogs97 opened 2 years ago

fernandogs97 commented 2 years ago

Hello, I am learning to perform models with your pipeline. While reading the article "Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics" one question came to my mind. It states that for each gene-tissue pair for which you had adjusted expression data, you fit an Elastic-Net model based on the genotypes of the samples for the SNPs located within 1 Mb upstream of the gene’s transcription start site and 1 Mb downstream of the transcription end site. I have been reading the code of this pipeline, and I do not understand where or how can I modify this "SNP window" upstream or downstream from TSS, there is any option for indicate this or you just modify the gene coordinates in the input data?

fernandogs97 commented 2 years ago

After reviewing againg your code, I´ve seen that it could be the parameter "cis_window" in the R code, am I right?, thank you very much in advance

Fnyasimi commented 2 years ago

Yes you are right

hakyim commented 1 year ago

Yes, that’s correct

On Wed, May 25, 2022 at 6:30 AM fernandogs97 @.***> wrote:

After reviewing againg your code, I´ve seen that it could be the parameter "cis_window" in the R code, am I right?, thank you very much in advance

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