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MATH-493
22 April
PCs in GWAS - Nature Genetics paper
PCs in GWAS - Nature Genetics paper
Click
price2006.pdf
link to view the file.
◄ GWAS-extras + data files
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Announcements
CRAN: The Comprehensive R Archive Network
R Studio downloads page
Quick-R home page
R Markdown: The Definitive Guide
R Markdown lessons from R Studio
knitr with R Markdown - Karl Broman's website
Forum: Finding group members
Video Lecture 1a
Lecture 1a slides - Reproducible Research
Video Lecture 1b (from end of Prob-Stat I)
Lecture 1b slides - Hypothesis testing review
Power example
Lab 1 - EDA (exploratory data analysis)
Installing R and RStudio
Getting started with R/RStudio
TP 0
Q+A Week 1
Video Lecture 2a
Video Lecture 2b
Lecture 2 slides
Lab 2a
Lab 2a - reponses to questions in class
Linear Models in R
Linear Statistical Models (MASS ch. 6)
Lab 2b (optional but strongly suggested - tutorial on R Markdown)
Q+A Week 2
Report 1 - Group / Data assignments
Report 1 criteria
Reports - ADDITIONAL TIPS
Q+A Report 1
Video Lecture 3a
Video Lecture 3b
Lecture 3 slides
Lab 3
Lab 3 - reponses to questions in class
Q+A Week 3
Video Lecture 4a
Video Lecture 4b
Lecture 4 slides
Lab 4
Lab 4 data
Q+A Week 4
Video Lecture 5a
Video Lecture 5b
Video Lecture 5c
Lecture 5 slides
Titanic example of logistic regression in R
Evaluating logistic regression models
Poisson regression in R
Lab 5
Lab 5 - responses to questions in class
Q+A Week 6
Study assessment questions
Video Lecture 6a
Video Lecture 6b
Lecture 6 slides
R Data Camp survival analysis tutorial
Cox ph modeling in R
My.stepwise R package
Lab 6
Comments Lab 6
Q+A Week 7
R1
R2
A1
A2
Late prelim reports (any)
Video Lecture 7a
Video Lecture 7b
Lecture 7 slides
Discrete data analysis with R
Lab 7
Additional comments labs 6+7
More on mosaic plots
Q+A Week 8
Video Lecture 8a (same as Statistical Genetics Lecture 4a)
Video Lecture 8b (same as Statistical Genetics Lecture 4b)
Video Lecture 8c
Lecture 8 slides
Lab 8a - PCA (OPTIONAL)
Food data
Lab 8b - Multiple testing (OPTIONAL)
GWAS-extras + data files
PCs in GWAS - slide presentation
Manhattan plot with -log10p on y-axis
GWASTools BioConductor R package (data cleaning/qc tools, maybe interesting)
Other tutorial for SNPRelate (possibly interesting, completely optional)
SNPassoc paper (optional but maybe useful)
SNPassoc R package (contains functions for eigenstrat, Cochran-Armitage (trend) test, etc.)
Lecture 9 slides (OPTIONAL)
Quick introduction to pwr package in R (OPTIONAL)
Lab 9 (OPTIONAL) - power tutorial
Lecture 10 slides (OPTIONAL)
Lab 10 (OPTIONAL)
Lecture 11 slides (OPTIONAL)
Lab 11 (OPTIONAL)
Logistic prelim report
GLM prelim report
Survival prelim report
Discrete prelim report
GWAS prelim report
Video Lecture 12a (OPTIONAL)
Video lecture 12b (OPTIONAL)
Lecture 12 slides (OPTIONAL)
Lab 12 (old lab 6) - OPTIONAL
Hierarchichal clustering in R
Heatmaps in R
Heatmaps in R - short tutorial
R graph gallery - heatmaps
article L1 - due 15 July 23.59
article L2 - due 15 July 23.59
PCs in GWAS - slide presentation ►
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