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CHUNKSIZE=250
NCHUNK=864
CHUNK=range(0,NCHUNK)


rule all:
	input:
		"instrument_specificity_analysis.html"

rule dl:

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---
title: Comparing survey answers before and after intervention
author: Gibran Hemani
---

```{r}
suppressMessages(suppressWarnings(suppressPackageStartupMessages({
	library(knitr)
	library(tidyverse)
})))

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---
title: Analysis of rs13107325 heterogeneity in BMI - osteoarthritis MR analysis
author: Gibran Hemani
date: "`r Sys.time()"
---

```{r}
library(tryx)
library(TwoSampleMR)
library(ieugwasr)

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---
title: Quick MR of fibronectin / cytokines / matrix metalloproteinases on osteoarthritis
date: "`r Sys.time()"
---


This paper presents a mathematical model linking osteoarthritis (OA) to a dynamic inflammation system involving cytokines and fibronectin https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5562782/.

Quick look at whether genetic relationships associate:

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library(gwasglue)
library(ieugwasr)
library(tidyverse)
library(susieR)
library(glue)

# DHA fine mapping
temp <- associations("11:61200000-62100000", "met-d-DHA")
ggplot(temp, aes(x=position, y=-log10(p))) +
geom_point()

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---
title: Comparison of effect allele frequencies in TwoSampleMR
author: Gibran Hemani
date: "`r Sys.time()`"
---


```{r, echo=FALSE}
library(knitr)
opts_chunk$set(warning=FALSE, message=FALSE)

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library(TwoSampleMR)
library(ieugwasr)
library(tidyverse)

# Get harmonised data for exposure and outcome
# e.g. BMI vs CHD
dat <- 	make_dat(exposures="ieu-a-2", outcomes="ieu-a-7")

# infer the AF for controls only for CHD
# first get case control sizes

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# on bc3

# wget https://fluff.bris.ac.uk/fluff/u2/mk19726/Al7MuuePNzS7tMWliJGG6QznF/fev1_adjusted_only_for_sex_imputed.txt
# wget https://fluff.bris.ac.uk/fluff/u2/mk19726/0ar7Sekl4I3Xj4JyatEf_wznc/fvc_adjusted_only_for_sex_imputed.txt
# wget https://fluff.bris.ac.uk/fluff/u4/mk19726/pUNC547Sala4I5Y1V_G9Bwzna/obstructive_ratio_spirometry_imputed.txt



# FEV1:
# sample size 353315

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library(GwasDataImport)
library(data.table)
library(ieugwasr)
library(dplyr)


# Download the Howard et al 2019 MDD GWAS from https://datashare.ed.ac.uk/handle/10283/3203
a <- data.table::fread("https://datashare.ed.ac.uk/bitstream/handle/10283/3203/PGC_UKB_depression_genome-wide.txt?sequence=3&isAllowed=y")

# It doesn't have chr/pos, so let's look them up on OpenGWAS (a bit slow!)

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---
title: Survival bias in sex association with dementia
author: Gibran Hemani
date: `r Sys.time()`
---

```{r}
library(dplyr)
library(tidyr)
library(ggplot2)