| # Load libraries | |
| library(TwoSampleMR) | |
| library(MRInstruments) | |
| # Load the ARIES mQTL catalog | |
| data(aries_mqtl) | |
| # Get the mQTLs from just one time point | |
| cpglist <- subset(aries_mqtl, age == "Childhood") |
| library(pwr) | |
| library(ggplot2) | |
| # calculate the minumum r2 that could be detected | |
| r2 <- pwr.r.test(n=c(100,200), power=0.8, sig.level=0.05/100000)$r^2 | |
| # | |
| dat <- expand.grid( |
| library(ggplot2) | |
| library(reshape2) | |
| makePhen <- function(effs, indep, vy=1, vx=rep(1, length(effs))) | |
| { | |
| if(is.null(dim(indep))) indep <- cbind(indep) | |
| stopifnot(ncol(indep) == length(effs)) | |
| stopifnot(length(vx) == length(effs)) | |
| cors <- effs * vx / sqrt(vx) / sqrt(vy) | |
| stopifnot(sum(cors^2) <= 1) |
| fastAssoc <- function(y, x) | |
| { | |
| index <- is.finite(y) & is.finite(x) | |
| n <- sum(index) | |
| y <- y[index] | |
| x <- x[index] | |
| vx <- var(x) | |
| vy <- var(y) | |
| bhat <- cov(y, x) / vx |
| --- | |
| title: Simulations of estimating genetic correlations on phenotypic principal components | |
| author: Gibran Hemani | |
| date: "`r Sys.Date()`" | |
| output: | |
| pdf_document: | |
| keep_tex: true | |
| --- | |
| **To reproduce this analysis, code is available here:** [ https://gist.github.com/617a64134f74b3ee8eaba704b8949284 ]() |
Introduction
Importance of imputation
| example code to share | |
| library(pROC) | |
| library(ggplot2) | |
| library(dplyr) | |
| library(tidyr) | |
| make_geno <- function(nid, nsnp, maf) | |
| { | |
| return(matrix(rbinom(nid * nsnp, 2, maf), nid, nsnp)) | |
| } |
| lsls |
| lsls |