---
title: "LD matrices"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{LD matrices}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval=FALSE
)
```


Components of GWAS summary data

- genome wide
- sample overlap
- distribution of genetic effects
	- polygenic
	- following an evolutionary model
- sparseness
- genetic effects wrt LD patterns
- winner's curse - top hits have winner's curse
- large sample sizes
- population structure


```{r setup}
library(simulateGP)
```

```{r}
pop <- "EUR"
bfile <- paste0("/Users/gh13047/repo/mr-base-api/app/ld_files/", pop)

varref <- variant_reference(bfile)
regions <- get_regions(pop)

t1 <- Sys.time()
generate_ld_matrices(regions[1:2,], varref, bfile)
Sys.time()-t1

t1 <- Sys.time()
generate_ld_matrices2(regions[1:2,], varref, bfile)
Sys.time()-t1
```