Tag: PRSice

How can I calculate PRS for all samples by using PRSice-2.

How can I calculate PRS for all samples by using PRSice-2. 0 Hi. I am trying to calculate PRS by using PRSice-2. I’d like to know how to handle the model. When I provide same gwas results to PRSice-2’s –base option, is the model always same? I have several thousands…

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PRSice-2 Documentation

PRSice-2 Documentation 1 Hi, Does anyone has detailed documentation of PRSice-2 software? The official website has been down for several weeks. Thank you! Mengna PRSice-2 • 69 views We lost the domain name because we forgot the login password… You can now revert to the repo doc (which is the…

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Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

Study population The study sample included 34,072 unrelated (3rd degree or less) TOPMed participants from eight U.S. based cohort studies: Jackson Heart Study (JHS; n = 2504), Framingham Heart Study (FHS; n = 3520), Hispanic Community Health Study/Study of Latinos (HCHS/SOL; n = 6,408), Atherosclerosis Risk in Communities study (ARIC; n = 6197), Cardiovascular Health Study (CHS; n = 2835),…

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Alternatives and detailed information of Prsice

PRSice (pronounced ‘precise’) is a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS). PRSice can run at high-resolution to provide the best-fit PRS as well as provide results calculated at broad P-value thresholds, illustrating results corresponding to either, can thin SNPs according to…

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Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing

** Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing ** The NeuroGenomics and Informatics (NGI) Center lead by Dr. Carlos Cruchaga at Washington University School of Medicine is recruiting a Bioinformatics Scientist to work on Whole Genome and Whole Exome Sequencing. We are seeking an experienced, self-motivated, self-driven scientist…

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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…

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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…

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How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice

How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice 1 This is a two part question. First, when implementing PRSice, is there a way to make sure certain SNPs are retained for the PRS calculation? I basically want to avoid…

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PRS from a dataset on which the GWAS is based on

PRS from a dataset on which the GWAS is based on 0 I am using the PRSice tool to calculate PRS scores for a dataset (d1) using a set of weights from the PGS catalog. Although the weights were generated from a different cohort (d2), it appears that the original…

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PRS using PGS Catalog

PRS using PGS Catalog 1 When using PRSice for PRS calculation of target data using a file of variants from the PGS catalog, does the variant file from the PGS catalog replace the GWAS summary statistics (referred to as “base data” in the tutorial)? I had previously found this similar…

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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…

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Validation in new sample

Validation in new sample 0 Hi Sam, I am trying to validate in a new sample a PRS I conceived by PRSice. I would like to ask if using snp_prs function (bigsnpr package in R) is a good way for that or should I use another tool or method. Best…

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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…

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Polygenic Risk Score Plot

Polygenic Risk Score Plot 0 I have a dataset of about 6000 people, Chromosome 21. I calculated PRS using plink and PRSice. The plot is shown above. I have two questions regarding this. R2 on the y-axis explains the phenotype variation, but I want another measure like AUC (area under…

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PRSice “command not found”

PRSice “command not found” 0 Hi all, When running PRSice (version 2.3.3), I got the “command not found” for the commands: –perm –thread –binary-target T How to make these commands working. Best regards, Redha Command • 17 views • link updated 1 hour ago by Sam ★ 3.7k • written…

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