Yuan Blog

PRS score (3)

using PRSice-2, lassosum

君子和而不同 This is the third part of the PRS blog, calculating PRS scores using PRSice2 and lassosum. Tip: Key point to calculate PRS The formula to calculate PRS score is given in "PRS score...

Posted by Yuan on May 31, 2022

jekyll theme information tags

note warning tip important callout

Fly high Jekyll provide flexible ways to write alert information in your markdown blogs. I choose the one contributed by tomjoht, which is the updated. Still, there is an order version, from ...

Posted by Yuan on May 29, 2022

jekyll markdown tabs

Using Navtabs

The palest ink is better than the best memory Github markdown tabs I tried some different implementations. Based on jekyll configs, Navtabs is most flexible to my knowlege, with least changes ...

Posted by Yuan on May 29, 2022

PRS score (2)

PRS calculation using plink

君子博学而日参省乎己，则知明而行无过矣 This is part 2 of PRS score calculation blog. The first part focuses on QC in base and target GWAS Required files Before calculating PRS scores, the following files are r...

Posted by Yuan on May 26, 2022

PRS score

A tutorial based on PLINK, PRSice 2, LDpred 2 and lassosum

My Weakness, My Strength Recently, I have genetic data to be added to my AD models. For each subject, I intended to add their PRS score of AD as a new feature. This blog is based on two tutor...

Posted by Yuan on May 24, 2022

Sampling Methods

MCMC and Beyond

学而时习之,不亦乐乎 Introduction Computer sampling provides revolutional tools to Bayesian statistics, where posterior distribution is not always directly available. In Bayesian philosophy, a parameter...

Posted by Yuan on February 22, 2022

Multiple Comparisons After ANOVA

with p adjusted

stay hungry ANOVA and post hoc ANOVA In an ANOVA experiment, if we got a pvalue indicating significant(reject null), we need go to pairwise comparisons to find out the extact pairs that showin...

Posted by Yuan on February 3, 2022

Eigengene: explaination and reproduce

WGCNA

wake up! Eigengene The concept of eigengene was first introduced by Orly et al. By definition, eigengenes are the right singular vectors of the SVD of the expression matrix(row as genes, colu...

Posted by Yuan on February 3, 2022

DataTable

withExamples

sweet! Data.table I’ve worked on large dataset for a long time. Previously, I mainly used dataframes to deal with various data manipulations and wranglings. It is OK and I got used to that. Ho...

Posted by Yuan on January 6, 2022

Views_and_Copies_in_pandas

explained_with_examples

You are furious because of ignorance Copies and views are very common in python, especially when you are working with arrays, lists, pandas. I’m aware of this, still, was trapped in a bug beca...

Posted by Yuan on January 5, 2022