The TwoSampleMR package is sitting here:
https://scmv-ieugit.epi.bris.ac.uk/gh13047/mr_base
The following people currently have access as 'Masters' on this repository:
- Gib Hemani
- Tom Gaunt
gibran hemani explodecomputer
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| load("aries_funnorm.randomeffect.pc10.160915.Robj") | |
| load("samplesheet_aries.160915.Robj") | |
| # Make sure that all the sample_names in samplesheet match the colnames in norm.beta.random | |
| all(samplesheet$Sample_Name == colnames(norm.beta.random)) | |
| # This is not the case so we need to match things up | |
| # Get the intersect | |
| ids <- intersect(samplesheet$Sample_Name, colnames(norm.beta.random)) |
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| library(reshape2) | |
| library(ggplot2) | |
| library(alspac) | |
| b <- findVars("bmi") | |
| b <- subset(b, cat2=="Clinic" & cat3 == "Child") | |
| bmi <- extractVars(b) | |
| c <- cor(bmi[,-c(1:3)], use="pair") |
explodecomputer
/ prediction.R
Created
November 12, 2015 23:07
Prediction using absolute values vs positive and negative values
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| m <- 100 | |
| n <- 100 | |
| eff <- rnorm(m) | |
| x <- matrix(rbinom(m*n,2,0.5), n, m) | |
| yhat <- x %*% eff | |
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| --- | |
| title: A frailty effect is sufficient to explain the apparent association of a smoking heaviness variant on smoking initiation in a cross sectional population | |
| date: "`r Sys.Date()`" | |
| output: pdf_document | |
| bibliography: smoking_age.bib | |
| --- | |
| ```{r, echo=FALSE} | |
| opts_chunk$set(warning=FALSE, message=FALSE, echo=FALSE) | |
| ``` |
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| arguments <- commandArgs(T) | |
| k <- as.numeric(arguments[1]) | |
| threshold <- as.numeric(arguments[2]) | |
| nfold <- as.numeric(arguments[3]) | |
| aries.release.dir <- "/panfs/panasas01/shared/alspac/deprecated/aries/releasev2_apr2014/" | |
| time.point <- "cord" ## "FOM","antenatal","cord","F7","15up" |
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| ($1 == 1) && ($4 >= 48287981) && ($4 <= 52287979) {print $2} | |
| ($1 == 2) && ($4 >= 86088343) && ($4 <= 101041482) {print $2} | |
| ($1 == 2) && ($4 >= 134666269) && ($4 <= 138166268) {print $2} | |
| ($1 == 2) && ($4 >= 183174495) && ($4 <= 190174494) {print $2} | |
| ($1 == 3) && ($4 >= 47524997) && ($4 <= 50024996) {print $2} | |
| ($1 == 3) && ($4 >= 83417311) && ($4 <= 86917310) {print $2} | |
| ($1 == 3) && ($4 >= 88917311) && ($4 <= 96017310) {print $2} | |
| ($1 == 5) && ($4 >= 44464244) && ($4 <= 50464243) {print $2} | |
| ($1 == 5) && ($4 >= 97972101) && ($4 <= 100472101) {print $2} | |
| ($1 == 5) && ($4 >= 128972102) && ($4 <= 131972101) {print $2} |
explodecomputer
/ filter_1kg.sh
Created
October 24, 2015 18:32
filtering 1kg data to hm3 and recoding snp names
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| #!/bin/bash | |
| module add apps/plink-1.90b3v | |
| cd /panfs/panasas01/shared/alspac/deprecated/gib/data_for_suzi | |
| cp /panfs/panasas01/shared/alspac/deprecated/alspac_combined_1kg_20140424/combined/alspac_1kg_p1v3_maf0.01_info0.8.bed als.bed | |
| cp /panfs/panasas01/shared/alspac/deprecated/alspac_combined_1kg_20140424/combined/alspac_1kg_p1v3_maf0.01_info0.8.bim als.bim | |
| cp /panfs/panasas01/shared/alspac/deprecated/alspac_combined_1kg_20140424/combined/alspac_1kg_p1v3_maf0.01_info0.8.fam als.fam |
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| # Suppose you have some files that look like this: | |
| # bmi_chr01.profile | |
| # bmi_chr02.profile | |
| # bmi_chr03.profile | |
| # etc | |
| # Read in each profile score | |
| l <- list() | |
| j <- 1 | |
| for(i in 1:22) |
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| library(ggplot2) | |
| library(devtools) | |
| library(reshape2) | |
| #install_github("brentp/celltypes450") | |
| library(celltypes450) | |
| library(meffil) | |
| options(mc.cores=16) | |
| # Using GSE55491 | |
| # Estimate cell counts using meffil |