---
title: "Looking up chromosome and position for large sets of rs IDs"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Looking up chromosome and position for large sets of rs IDs}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

Often GWAS datasets are shared with only the rs ID. To upload to the OpenGWAS database we need chromsome, position, effect allele, non-effect allele - rs ID is not used primarily. 

The `get_positions()` function provides a convenient way to just lookup the chromosome and position from rs ID, though be warned it is quite slow, e.g. might take up to 30 minutes for 10 million SNPs.

```{r setup}
library(GwasDataImport)
library(data.table)

# Read in a small dataset
fn <- system.file("extdata/pos_0002.txt.gz", package="GwasDataImport")
a <- fread(fn)

# list of rsids
rsid <- a$RSID

# get positions
pos <- get_positions(rsid)
```