𝕤interactive GCTA tutorial We’ll follow the GCTA tutorial here Read more →

ℝeview of maximum likelihood estimation […] Review of logistic regression […] Learn the basics of the command line […] Learn the basics of R […] Get Rstudio and the command line set up […] … Read more →

𝕎e want to calculate the power to detect an association a genetic marker and a quantitative phenotype. […] As a concrete example, we pre-specify the model for continuous trait \(Y\) and genotype \(X\) as \[Y = \beta X + \epsilon, ~~~~ \text{with } \epsilon \sim N(0, \sigma_\epsilon^2)\] where … Read more →

\[ \newcommand{\E}{\text{E}} \] […] This is a minial tutorial on using ldsc for LDSC regression. Let’s start by reviewing what LDSC regression does and what kind of input files are required for a minimal LDSC regression analysis. Under polygenic model, B. K. Bulik-Sullivan et al. (2015) … Read more →

ℂreated by Yanyu Liang, with some material adapted from Charles Washington III and Jiamao Zheng’s lab 6 from 2018 As we know that eQTL analysis needs to test association for each gene in transcriptome against a set of variants. Typically, for cis-eQTL analysis, one gene could have thousands of … Read more →

ℂreated by Max Winston; modified by Charles Washington III, Ankeeta Shah, and Yanyu Liang This class is designed to introduce a variety of concepts, methods, and tools utilized in statistical genetics. The majority of tools used to employ these methods and concepts require basic knowledge of … Read more →

𝕋o recap, S-PrediXcan analysis takes GWAS summary statistics, gene expression prediction models (weights for SNPs), and reference LD and provides gene-level association between predicted expression and trait. So, it requires the following three pieces of data: […] The complete analysis … Read more →

𝕙ttps://docs.google.com/presentation/d/16aMKkcAX1QifQabgBSBR_xr8LuoLwnsj9eEBFXi6EYk/edit?usp=sharing […] See slides Read more →

𝕀n this lab we are going to use the PRSice software to take height GWAS results and predict height of the Personal Genome Project individuals using their genotype data. Goals […] library(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ## ✓ … Read more →

𝕤uppressMessages(library(tidyverse)) suppressMessages(library(glue)) PRE = "/Users/haekyungim/Library/CloudStorage/Box-Box/LargeFiles/imlab-data/data-Github/web-data" ## COPY THE DATA AND SLUG FROM THE HEADER DATA = glue("{PRE}/2022-04-20-gwas-catalog-analysis-2022") … Read more →