explodecomputer

Working on MR base

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

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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}

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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

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manifest <- read.table("manifest.file")

# make sure IDs in manifest are matched to IDs in cpg matrix

tbetas_fom_subset <- t(tbetas[cpgs,])

tbetas_fom_subset[, 1] <- residuals(lm(tbetas_fom_subset[, 1] ~ manifest[,1:5]))
tbetas_fom_subset[, 2] <- residuals(lm(tbetas_fom_subset[, 2] ~ manifest[,1:5]))
tbetas_fom_subset[, 3] <- residuals(lm(tbetas_fom_subset[, 3] ~ manifest[,1:5]))

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here is a gist

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# Some example data
# Data frame with an id column
data1 <- data.frame(ids = c("A", "B", "C"), value = 1:3)

# matrix with rownames for ids
data2 <- matrix(1:20, 4, 5)
rownames(data2) <- c("C", "D", "B", "E")

# Get data1 into the same order as data2

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newmat <- as.data.frame(t(mat))
newmat$ALN <- rownames(newmat)
combineddata <- merge(bmi, newmat, by="ALN")


# See if they are individually associated with BMI

model <- lm(bmi ~ cpg1)