---
title: "Import GWAS summary statistics from Open GWAS"
author: "<h5><i>Authors</i>: Alan Murphy, Brian Schilder and Nathan Skene</h5>"
date: "<h5><i>Updated</i>: `r format(Sys.Date(), '%b-%d-%Y')`</h5>"
csl: nature.csl
output:
  BiocStyle::html_document:
vignette: >
    %\VignetteIndexEntry{OpenGWAS} 
    %\usepackage[utf8]{inputenc}
    %\VignetteEngine{knitr::rmarkdown}
---

```{r style, echo=FALSE}
knitr::opts_chunk$set(tidy = FALSE,
                      message = FALSE)
```

```{r}
library(MungeSumstats)
```

MungeSumstats now offers high throughput query and import functionality to data 
from the MRC IEU [Open GWAS Project](https://gwas.mrcieu.ac.uk/).


# Find GWAS datasets 

```{r,eval=FALSE}
#### Search for datasets ####
metagwas <- MungeSumstats::find_sumstats(traits = c("parkinson","alzheimer"), 
                                         min_sample_size = 1000)
head(metagwas,3)
ids <- (dplyr::arrange(metagwas, nsnp))$id  
```

```{r,echo=FALSE}
#### Search for datasets ####
#error_dwnld <-
#            tryCatch(
#              metagwas <- MungeSumstats::find_sumstats(traits = c("parkinson",
#                                                                  "alzheimer"), 
#                                         min_sample_size = 1000),
#            error = function(e) e,
#            warning = function(w) w
#            )
#if(exists("metagwas")&&is.data.frame(metagwas)){#if exists downloaded fine
#  head(metagwas,3)
#  ids <- (dplyr::arrange(metagwas, nsnp))$id  
#}

#to speed up build just create results
metagwas2 <- 
    data.frame(
        id=c("ieu-a-298","ieu-b-2","ieu-a-297"),
        trait = rep("Alzheimer's disease",3),
        group_name = rep("public",3),
        year=c(2013, 2019, 2013),
        author=c("Lambert","Kunkle BW","Lambert"),
        consortium=c("IGAP",
                     "Alzheimer Disease Genetics Consortium (ADGC), European Alzheimer's Disease Initiative (EADI), Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (CHARGE), Genetic and Environmental Risk in AD/Defining Genetic, Polygenic and Environmental Risk for Alzheimer's Disease Consortium (GERAD/PERADES),",
                     "IGAP" ),
        sex=rep("Males and Females",3),
        population=rep("European",3),
        unit=c("log odds","NA","log odds"),
        nsnp=c(11633,10528610,7055882),
        sample_size=c(74046,63926,54162),
        build=rep("HG19/GRCh37",3),
        category=c("Disease","Binary","Disease"),
        subcategory=rep("Psychiatric / neurological",3),
        ontology=rep("NA",3),
        mr=rep(1,3),
        priority=c(1,0,2),
        pmid=c(24162737,30820047,24162737),
        sd=rep(NA,3),
        note=c("Exposure only; Effect allele frequencies are missing; forward(+) strand",
               "NA","Effect allele frequencies are missing; forward(+) strand"),
        ncase=c(25580,21982,17008),
        ncontrol=c(48466,41944,37154),
        N=c(74046,63926,54162)
    )
print(head(metagwas2,3))
```

# Import full results

You can supply `import_sumstats()` with a list of as many OpenGWAS IDs as you 
want, but we'll just give one to save time. 

```{r,eval=FALSE}
datasets <- MungeSumstats::import_sumstats(ids = "ieu-a-298",
                                           ref_genome = "GRCH37")
```

```{r,echo=FALSE}
#don't actually run as this takes some time, use stashed version
datasets <- list("ieu-a-298"=paste0(tempdir(),"/ieu-a-298.tsv.gz"))
#stashed value
datasets_data <- list("ieu-a-298"=system.file("extdata","ieu-a-298.tsv.gz",
                                                package="MungeSumstats"))

```

## Summarise results 

By default, `import_sumstats` results a named list where the names are the Open 
GWAS dataset IDs and the items are the respective paths to the formatted summary
statistics.

```{r}
print(datasets)
```

You can easily turn this into a data.frame as well. 

```{r}
results_df <- data.frame(id=names(datasets), 
                         path=unlist(datasets))
print(results_df)
```




# Import full results (parallel)

*Optional*: Speed up with multi-threaded download via [axel](https://github.com/axel-download-accelerator/axel).  

```{r, eval=FALSE}
datasets <- MungeSumstats::import_sumstats(ids = ids, 
                                           vcf_download = TRUE, 
                                           download_method = "axel", 
                                           nThread = max(2,future::availableCores()-2))
```

# Further functionality

See the [Getting started vignette](https://neurogenomics.github.io/MungeSumstats/articles/MungeSumstats.html)
for more information on how to use MungeSumstats and its functionality.


# Session Info

<details>

```{r}
utils::sessionInfo()
```

</details>