𝕒lpha = 0.05 Patleastonemistake = function(m) {1 - (1-alpha)^m} curve(Patleastonemistake,from = 1, to=100, ylab="Prob at least one wrong", xlab="m = number of tests") grid() abline(h=1,col='gray') Read more →

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𝕝ibrary(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ── ## ✓ ggplot2 3.3.3 ✓ purrr 0.3.4 ## ✓ tibble 3.0.5 ✓ dplyr 1.0.3 ## ✓ tidyr 1.1.2 ✓ stringr 1.4.0 ## ✓ readr 1.4.0 ✓ forcats 0.5.0 ## ── Conflicts ────────────────────────────────────────── … Read more →

𝕝ibrary(tidyverse) work.dir ="~/Downloads/hapmap/" ## qqunif function source("https://gist.githubusercontent.com/hakyim/38431b74c6c0bf90c12f/raw/21fbae9a48dc475f42fa60f0ef5509d071dea873/qqunif") Download plink for mac ## Download plink from https://www.cog-genomics.org/plink2 ## … Read more →

𝕝ibrary(tidyverse) ## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ── ## ✓ ggplot2 3.3.3 ✓ purrr 0.3.4 ## ✓ tibble 3.0.5 ✓ dplyr 1.0.3 ## ✓ tidyr 1.1.2 ✓ stringr 1.4.0 ## ✓ readr 1.4.0 ✓ forcats 0.5.0 ## ── Conflicts ────────────────────────────────────────── … Read more →

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ℍere are the slides for today download link […] can be used to calculate chip heritability, genetic correlation between traits, and to attribute the inflation of summary statistics from GWAS to either polygenicity (true causal effect) or confounding due to population structure or other … Read more →

𝕙ttps://uchicago.box.com/s/iqxg6yo7pi50hyudnfcv2xnhtfp6euv8 […] 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, let’s do the … Read more →

𝕋he GWAS assumption is \(\boldsymbol{Y} = \boldsymbol{X}\beta + \boldsymbol{\epsilon}\) Example with n=4 \[\begin{bmatrix} y_1 \\ y_2 \\ y_3 \\ y_4 \end{bmatrix} = \begin{bmatrix} x_1 \\ x_2 \\ x_3 \\ x_4 \end{bmatrix}\cdot \beta + \begin{bmatrix} \epsilon_1 \\ \epsilon_2 \\ \epsilon_3 \\ \epsilon_4 … Read more →