Lab 3 - PCA - GCTA

Haky Im

2021-04-16

Categories: lab

Learning Objectives

Calculate heritability with GCTA
Perform PCA

Remarks

Do not run large processes on the head node of a HPC cluster. You can use the interactive mode. Find more info on using Midway here

sinteractive

GCTA tutorial

We’ll follow the GCTA tutorial here

Homework

Run LD Score regression
Calculate GRM of 6 hapmap individuals and show the tileplot

Reuse

Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

Suggest changes

If you find any mistakes (including typos) or want to suggest changes, please feel free to edit the source file of this page on Github and create a pull request.

Citation

For attribution, please cite this work as

Haky Im (2021). Lab 3 - PCA - GCTA. BIOS 25328 Cancer Genomics Class Notes. /post/2021/04/16/lab-3-pca-gcta/

BibTeX citation

@misc{
  title = "Lab 3 - PCA - GCTA",
  author = "Haky Im",
  year = "2021",
  journal = "BIOS 25328 Cancer Genomics Class Notes",
  note = "/post/2021/04/16/lab-3-pca-gcta/"
}