Questions tagged [polygenic-risk-score]
The polygenic-risk-score tag has no usage guidance.
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Can the PGS Calculator give the contribution of each variant to the overall PGS?
I am using the PGS Calculator (https://github.com/PGScatalog/pgsc_calc/) to compute the polygenic scores of individuals based on a scoring file.
PGS Calculator works wonderfully and outputs the ...
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How to associate point mutations to quantitative protein levels
My experiment is based on a quantitative continuous variable levels (B12 vitamin) in a sample of patients retrospectively selected based on values that can take (under our criteria):
normal
low ...
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Input for --score in PLINK 1.9 when generationg PRS using GWAS summary statistics
I'm conducting a simulation and I need to obtain polygenic risk scores (PRS) using genome wide association studies (GWAS) summary statistics.
It is known that the GWAS will give BETA and OR for ...
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Polygenic Risk score calculation using vcf files
I have about 750 vcf files and I am looking to generate a Polygenic Risk Score for each individual. I am planning to use either PLINK or LDPhred to generate a Risk Score. I have phenotype information ...
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Summary statistics version problem
I am learning GWAS study and PRS for predicting disease. I was aligning my sequencing data with GRCH38 reference panel. However, in the PRS analysis step, I found that most of the summary statistics ...
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Polygenic Risk Scores
I have run a GWAS and used PRSice (https://www.prsice.info/) to calculate polygenic risk scores on the data collected from the GWAS. I need to check whether alcohol dependence can predict gambling ...
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Loss of predictive power of polygenic risk score when dataset contains missing variants
I am trying to calculate polygenic risk scores (PRS) scores for a new dataset. This dataset does not have all the variants that the PRS score needs. The PRS score I am interested in has 40 variants, ...
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