Tag: PRS

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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[ifsheldon/stannum] Proxy `torch.nn.Parameter` in `Tin` for PyTorch optimizers

Now Tin is a subclass of torch.nn.Module and it can have learnable parameters in the form of values in Taichi fields. However, now these values cannot be optimized by PyTorch optimizers, since they are not PyTorch-compatible. One way to make them to be PyTorch-compatible is to use a proxy torch.nn.Parameter…

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Auto updating website that tracks closed & open issues/PRs on scikit-learn/scikit-learn.

Live webpage Auto updating website that tracks closed & open issues/PRs on scikit-learn/scikit-learn. Running locally Setup a virtual environment. Install requirements pip install -r requirements Create a personal access token and set it to GITHUB_TOKEN. Run the following to call the GitHub API for repo information and cache the results…

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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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Real-World Study of Tisagenlecleucel in R/R B-Cell Non-Hodgkin Lymphomas Shows Efficacy, Safety

Real-world data on tisagenlecleucel in patients with relapsed/refractory B-cell lymphoma was consistent with the phase 2 JULIET trial, demonstrating favorable efficacy and safety. Real-world data on the use of tisagenlecleucel (Kymriah) showed greater efficacy and a favorable safety profile, according to updated findings from a study of the Center for…

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[BUG] (python-fastapi) OneOf class not generated

Bug Report Checklist Description For oneOf fields, the python-fastapi server generator creates a function that returns a OneOf* class, but that class itself is not generated. For example, for an API like /status: get: summary: Get the status of the upstream server responses: 200: description: successful operation content: application/json: schema:…

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[BUG] [Java] Model doesn’t build when using anyof / oneof and a primitive type

I have a schema like so: openapi: 3.0.3 info: title: java codegen BUG description: oneOf generates incorrect model for primitive types version: 1.0.0 paths: /openapi/example/path: post: requestBody: content: application/json: schema: $ref: ‘#/components/schemas/Request’ responses: 200: description: OK content: application/json: schema: $ref: ‘#/components/schemas/Response’ components: schemas: MyString: type: string MySpecialString: anyOf: – $ref:…

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Polygenetic Risk Score Calculation

Polygenetic Risk Score Calculation 1 Hello all, My company has Whole exome sequencing (WES) data for individuals lying around and was wondering if this can be used to generate Polygenetic Risk Scores (PRS)? From what I researched online, it seems to be more so used for GWAS and not WES….

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RStudio AI Weblog: Coaching ImageNet with R

ImageNet (Deng et al. 2009) is a picture database organized in keeping with the WordNet (Miller 1995) hierarchy which, traditionally, has been utilized in pc imaginative and prescient benchmarks and analysis. Nonetheless, it was not till AlexNet (Krizhevsky, Sutskever, and Hinton 2012) demonstrated the effectivity of deep studying utilizing convolutional…

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Why some SNP’s are not assigned to any gene?

Why some SNP’s are not assigned to any gene? 0 Hi everyone, I am doing polygenic risk analysis (PRS) ; As you may know PRS is done based on SNP’s. On the other hand, I would like to do some visualizations at gene level. Thus, I used rsnps library (ncbi_snp_query…

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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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How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual?

How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual? 2 Hi all, I have an annotated vcf file for one individual which I want to estimate his polygenic risk score (PRS) for a certain trait, using the scoring files from the PGSCatalog. The…

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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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