Introduction to Statistical Genetics (HGEN 47100 / BIOS 21216)
This course covers core concepts and statistical procedures that are used in the mapping of genetic traits from observational data. Students will learn basic statistical techniques of genome-wide association studies, tools for ``post-GWAS'' analysis and topics related to analysis of sequencing data.
partitioning heritability
2022-02-22
Festus Nyasimi
𝕀n this exercise, you will use LD score regression method to calculate the partitioned heritability of GWAS phenotype from UK Biobank.
Below is a step by step guide on setting up and running the analysis.
[…] If you have conda installed on your machine skip this step
Installation
[…] …
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Lecture 12: Integrating GWAS with QTL analysis
2022-02-21
Haky Im
𝔽ind the slides here
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Lecture 10 - PRS - Large scale mixed effects modelign
2022-02-13
Haky Im
𝔽ind slides here
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Homework 5
2022-02-09
Haky Im
𝕋he genetic relatedness matrix (which can be used to calculate heritability and also to adjust for relatedness and population structure) encodes the structure of the data. To get an intuitive sense of how that works, do the following.
[…] (10 points) Calculate GRM of hapmap_chr22 data …
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Lecture 9 - Mixed Effects Models - LD Score Regression
2022-02-09
Haky Im
𝔽ind the class notes here
[…] Example of mixed effects model to account for population structure
[…] Relating Z-scores, p-values, and chi2
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Review of connection between z-score, p-value, and chi2 stat
2022-02-09
Haky Im
ℕotice that the estimated effect size divided by the standard error behaves like a normal(0,1) random variable when the sample size is large enough:
[…] \[ Z = \frac{\hat\beta}{\text{se}(\hat\beta)}\] \[Z \approx N(0,1) ~~~~~~ \text{as } n \rightarrow \infty\] Let’s simulate zscore vector …
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Homework 4 - Population Structure
2022-02-03
Haky Im
𝕋otal of 40 points
Download hapmap3 data in plink format from https://uchicago.box.com/s/84de60jj4j9nyhl7nc7lylk4fcq12eka
[…] Hint: you can borrow code with the appropriate modifications from https://hgen471.hakyimlab.org/post/2021/02/18/l6-population-structure/
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Download and format HapMap data
2022-02-02
Haky Im
𝕨ork.dir = "~/Downloads/tempo/" knitr::opts_knit$set(root.dir = normalizePath(work.dir)) library(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ## ✓ ggplot2 3.3.5 ✓ purrr 0.3.4 ## ✓ tibble 3.1.6 ✓ dplyr 1.0.7 ## ✓ tidyr 1.1.4 ✓ stringr 1.4.0 …
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Lecture 7 - Population Structure
2022-02-01
Haky Im
𝕙ttps://www.icloud.com/keynote/0b9pu78RBdrSGsSRVCUWkNahg#2022-L7-Population-Structure
I’ve also uploaded a powerpoint version on canvas Module/lecture 7 as a backup.
[…] Mills, Melinda C.; Barban, Nicola; Tropf, Felix C.. An Introduction to Statistical Genetic Data Analysis (p. 237). …
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Homework 3 - Power Calculator
2022-01-25
Haky Im
ℕOTE: Go to this link
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