Tag: PRSice-2
How to find out why PRSice-2 excludes ambiguous SNPs
How to find out why PRSice-2 excludes ambiguous SNPs 0 When I use PRSice to calculate PRS，it alerts it excludes 25 SNPs from the base data. But how could I know the reason why they are ambiguous? Could I explore more why they are ambiguous? Question2: If I use PRSice…
Do we need to apply the same p-value threshold on all 22 chromsomes?
Polygenic Risk Score Calculation: Do we need to apply the same p-value threshold on all 22 chromsomes? 1 Hi there, I am using PRSice-2 to calculate the polygenic risk score for 22 chromosomes one by one. To my understanding, since the 22 chromosomes are independent of each other, and our…
PRS in UK Biobank – no covariate file and no phenotype file
PRS in UK Biobank – no covariate file and no phenotype file 1 Hi there, I am trying to undertake a PRS using UK Biobank plink data. I am trying to generate a PRS using PRSice-2. However, the issue I am having is that I do not have a covariate…
PRSice-2 without Ref SNP ID
PRSice-2 without Ref SNP ID 1 Does PRSice-2 support a base tile that has chromosome number/name and chromosome position instead of reference SNP ID in the base file? I’m trying to calculate PRS scores using a weights file from the PGS catalog with ~6 million variants. The file has only…
