### General API Query (GET)

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Perform a GET request to an API endpoint. This example queries for specific rsids in given studies.

```r
api_query("associations/ieu-a-2,ieu-a-7/rs234,rs123")
```

--------------------------------

### Install ieugwasr from GitHub

Source: https://mrcieu.github.io/ieugwasr/index.html

Install the developer version of the ieugwasr package directly from its GitHub repository.

```r
remotes::install_github("mrcieu/ieugwasr")
```

--------------------------------

### Install ieugwasr from CRAN

Source: https://mrcieu.github.io/ieugwasr/index.html

Install the stable version of the ieugwasr package from CRAN.

```r
install.packages("ieugwasr")
```

--------------------------------

### Install PLINK binary using genetics.binaRies

Source: https://mrcieu.github.io/ieugwasr/articles/local_ld.html

Installs the PLINK binary and retrieves it for use with ieugwasr functions. This is a prerequisite for running local LD operations.

```R
remotes::install_github("MRCIEU/genetics.binaRies")
genetics.binaRies::get_plink_binary()
```

--------------------------------

### Install ieugwasr from MRCIEU r-universe

Source: https://mrcieu.github.io/ieugwasr/index.html

Install the ieugwasr package from the MRCIEU r-universe repository, which may contain newer versions.

```r
install.packages('ieugwasr', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))
```

--------------------------------

### user()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Get user details.

```APIDOC
## user()

### Description
Get user details.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get available batches

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Retrieves a list of available batches and their descriptions from the OpenGWAS database.

```r
batches()
```

--------------------------------

### batches()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Get list of data batches in IEU OpenGWAS database.

```APIDOC
## batches()

### Description
Get list of data batches in IEU OpenGWAS database.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get List of Data Batches

Source: https://mrcieu.github.io/ieugwasr/reference/batches.html

Fetches a list of all available data batches from the IEU OpenGWAS database. Authentication may be required for certain endpoints.

```APIDOC
## Get list of data batches in IEU OpenGWAS database

### Description
Retrieves a list of all available data batches in the IEU OpenGWAS database.

### Method
GET

### Endpoint
/batches

### Parameters
#### Query Parameters
- **opengwas_jwt** (string) - Optional - Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.

### Response
#### Success Response (200)
- **data** (data frame) - A data frame containing information about the data batches.

### Request Example
```
GET /batches?opengwas_jwt=YOUR_JWT_TOKEN
```

### Response Example
```json
{
  "data": [
    {
      "batch_id": "1000",
      "batch_name": "1000 Genomes",
      "description": "Phase 3 data from 1000 Genomes Project"
    },
    {
      "batch_id": "ukbb",
      "batch_name": "UK Biobank",
      "description": "Subset of UK Biobank data"
    }
  ]
}
```
```

--------------------------------

### Get GWAS file download URLs

Source: https://mrcieu.github.io/ieugwasr/reference/gwasinfo_files.html

Use gwasinfo_files to get a list of download URLs for files like VCF, TBI, and HTML reports associated with a GWAS dataset. URLs expire in 2 hours. Ensure you have access to the dataset.

```R
gwasinfo_files(id, opengwas_jwt = get_opengwas_jwt(), ...)
```

--------------------------------

### gwasinfo_files()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Get list of download URLs for each file associated with a dataset through API.

```APIDOC
## gwasinfo_files()

### Description
Get list of download URLs for each file associated with a dataset through API.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get LD matrix using local PLINK binary and reference dataset

Source: https://mrcieu.github.io/ieugwasr/reference/ld_matrix_local.html

Use this function to compute the LD matrix locally. Specify the path to your PLINK binary and reference panel (bed/bim/fam files).

```R
ld_matrix_local(variants, bfile, plink_bin, with_alleles = TRUE)
```

--------------------------------

### Get User Details

Source: https://mrcieu.github.io/ieugwasr/reference/user.html

Retrieves details about the authenticated user. Authentication is handled via an OpenGWAS JWT.

```APIDOC
## Get User Details

### Description
Retrieves details about the authenticated user.

### Method
GET

### Endpoint
/user

### Parameters
#### Query Parameters
- **opengwas_jwt** (string) - Optional - Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.

### Response
#### Success Response (200)
- **user information** (object) - Contains the user's details.
```

--------------------------------

### Get All Available Studies

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Retrieve a list of all studies available through the OpenGWAS API.

```r
gwasinfo()
```

--------------------------------

### ld_matrix()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Get LD matrix for list of SNPs.

```APIDOC
## ld_matrix()

### Description
Get LD matrix for list of SNPs.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get Variant Info by rsID

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Retrieve variant information by providing a list of rsIDs.

```r
b <- variants_rsid(c("rs234", "rs333"))
```

--------------------------------

### gwasinfo()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Get list of studies with available GWAS summary statistics through API.

```APIDOC
## gwasinfo()

### Description
Get list of studies with available GWAS summary statistics through API.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get API Status

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Check the current status of the OpenGWAS API. Requires the ieugwasr library to be loaded.

```r
library(ieugwasr)
api_status()
```

--------------------------------

### Get User Details - ieugwasr

Source: https://mrcieu.github.io/ieugwasr/reference/user.html

Retrieves user details by authenticating with an OpenGWAS JWT. The JWT can be provided directly or set via the OPENGWAS_JWT environment variable.

```R
user(opengwas_jwt = get_opengwas_jwt())
```

--------------------------------

### Get 1000 Genomes Annotations by Position

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Retrieve 1000 Genomes population annotations for a specified genomic position or region.

```r
afl2_chrpos("1:100000-900000")
```

--------------------------------

### Print GWAS Information (R)

Source: https://mrcieu.github.io/ieugwasr/reference/print.GwasInfo.html

This is the S3 method for printing objects of class 'GwasInfo'. It is automatically called when you print the output of the gwasinfo function. No specific setup is required beyond obtaining the GwasInfo object.

```R
print(x, ...)
```

--------------------------------

### Get 1000 Genomes Annotations for Common Variants

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Extract 1000 Genomes annotations for a list of 20,000 variants that are common across all super populations and evenly spaced across the genome.

```r
afl2_list()
```

--------------------------------

### Get list of studies with available GWAS summary statistics

Source: https://mrcieu.github.io/ieugwasr/reference/gwasinfo.html

Retrieve all available GWAS summary statistics datasets by calling gwasinfo without any arguments. Authentication may be required for protected endpoints.

```R
gwasinfo(id = NULL, opengwas_jwt = get_opengwas_jwt(), ...)
```

--------------------------------

### Get Tophits from a Study

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Retrieve the top associated variants (tophits) from a specified GWAS study. Strict clumping is applied by default.

```r
tophits(id = "ieu-a-2")
```

--------------------------------

### Get list of data batches

Source: https://mrcieu.github.io/ieugwasr/reference/batches.html

Call the `batches` function to retrieve a data frame of available GWAS data batches. Authentication is handled by `opengwas_jwt`, which can be obtained from the OpenGWAS API or set as an environment variable.

```r
batches(opengwas_jwt = get_opengwas_jwt(), ...)
```

--------------------------------

### Get Top Hits from GWAS Dataset

Source: https://mrcieu.github.io/ieugwasr/reference/tophits.html

Use this function to obtain top genetic hits from GWAS studies. It supports server-side clumping by default. Specify GWAS study IDs, p-value thresholds, clumping parameters (r2, kb), and reference population.

```R
tophits(
  id,
  pval = 5e-08,
  clump = 1,
  r2 = 0.001,
  kb = 10000,
  pop = "EUR",
  force_server = FALSE,
  opengwas_jwt = get_opengwas_jwt(),
  ...
)
```

--------------------------------

### Get list of studies with available GWAS summary statistics

Source: https://mrcieu.github.io/ieugwasr/reference/gwasinfo.html

Retrieves a dataframe containing details for all available GWAS studies. If an ID is provided, it returns details for that specific study. Otherwise, it returns all available datasets.

```APIDOC
## Get list of studies with available GWAS summary statistics through API

### Description
Retrieves a dataframe of details for all available studies. If `id` is `NULL`, it retrieves all available datasets. Otherwise, it retrieves details for the specified OpenGWAS IDs.

### Method
GET

### Endpoint
/gwasinfo

### Parameters
#### Query Parameters
- **id** (string or list of strings) - Optional - List of OpenGWAS IDs to retrieve.
- **opengwas_jwt** (string) - Optional - Used to authenticate protected endpoints. Obtain a JWT from https://api.opengwas.io. Can also be stored in .Renviron as OPENGWAS_JWT.

### Response
#### Success Response (200)
- **data** (dataframe) - A dataframe containing details for all available studies.

### Request Example
```R
# Get all available studies
gwasinfo()

# Get a specific study by ID
gwasinfo(id = "GCST000001")
```

### Response Example
```json
[
  {
    "trait": "Alzheimer's disease",
    "study_accession": "GCST000001",
    "year": 2013,
    "author": "Sando et al.",
    "publication": "Nature Genetics",
    "journal_url": "http://www.nature.com/articles/ng.2585",
    "pubmedid": "23455511",
    "trait_reported": "Alzheimer's disease",
    "trait_mapped": "Alzheimer's disease",
    "trait_uri": "MONDO:0005136",
    "genome_build": "GRCh37",
    "ancestry_reported": "European",
    "ancestry_inference": "unknown",
    "ancestry_summary": "European",
    "ancestry_ncase": 13268,
    "ancestry_ncontrol": 29374,
    "ancestry_total": 42642,
    "unit": "log (OR)",
    "beta_unit": "log (OR)",
    "p_unit": "P",
    "ncase": 13268,
    "ncontrol": 29374,
    "total_sample_size": 42642,
    "download_url": "/downloads/GCST000001.tsv.gz",
    "source": "GWAS Catalog"
  }
  // ... more studies
]
```
```

--------------------------------

### Get LD matrix for list of SNPs

Source: https://mrcieu.github.io/ieugwasr/reference/ld_matrix.html

This function takes a list of SNPs and searches for them in a specified super-population in the 1000 Genomes phase 3 reference panel. It then creates an LD matrix of r values (signed, and not squared). All LD values are with respect to the major alleles in the 1000G dataset. You can specify whether the allele names are displayed.

```APIDOC
## ld_matrix

### Description
Generates an LD matrix for a given list of SNPs using a specified reference population.

### Usage
```R
ld_matrix(
  variants,
  with_alleles = TRUE,
  pop = "EUR",
  opengwas_jwt = get_opengwas_jwt(),
  bfile = NULL,
  plink_bin = NULL,
  ...
)
```

### Arguments
*   **variants** (list) - Required. A list of SNP rsids.
*   **with_alleles** (boolean) - Optional. Whether to append allele names to SNP names. Defaults to `TRUE`.
*   **pop** (string) - Optional. The super-population to use as a reference panel. Defaults to "EUR". Options include "EUR", "SAS", "EAS", "AFR", "AMR", and "legacy".
*   **opengwas_jwt** (string) - Optional. JWT for authenticating protected endpoints. Can be obtained from https://api.opengwas.io or set in .Renviron.
*   **bfile** (string) - Optional. Path to a local Bfile for API usage. Defaults to `NULL`.
*   **plink_bin** (string) - Optional. Path to the PLINK binary. If `NULL` and `bfile` is not `NULL`, the packaged PLINK binary for the OS will be detected. Defaults to `NULL`.
*   **...** - Additional arguments passed to `ld_matrix_api()`.

### Value
Matrix of LD r values.

### Details
The LD matrix generation uses bi-allelic SNPs with MAF > 0.01. Variants not meeting these criteria or absent from the reference panel will be excluded. Use `ld_reflookup()` to check variant presence. This function can be resource-intensive on OpenGWAS servers and is limited to 500 variants per call. Local execution is possible using `ld_matrix()` and related vignettes.
```

--------------------------------

### Get LD matrix for list of SNPs

Source: https://mrcieu.github.io/ieugwasr/reference/ld_matrix.html

Use this function to obtain an LD matrix for a list of SNPs. It defaults to using the EUR super-population from the 1000 Genomes reference panel and includes allele names in the output. Authentication via opengwas_jwt is required for protected endpoints.

```R
ld_matrix(
  variants,
  with_alleles = TRUE,
  pop = "EUR",
  opengwas_jwt = get_opengwas_jwt(),
  bfile = NULL,
  plink_bin = NULL,
  ...
)
```

--------------------------------

### select_api

Source: https://mrcieu.github.io/ieugwasr/reference/select_api.html

Toggles the API address between development and release versions.

```APIDOC
## select_api

### Description

Toggles the API address between development and release versions.

### Usage

```R
select_api(where = "public", silent = FALSE)
```

### Arguments

*   **where** (character) - Which API to use. Choice between `"public"`, `"private"`, `"dev1"`, `"dev2"`. Default = `"public"`.
*   **silent** (logical) - Silent? Default = `FALSE`.

### Value

No return value, called for side effects.
```

--------------------------------

### logging_info()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Details of how access token logs are used.

```APIDOC
## logging_info()

### Description
Details of how access token logs are used.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### print(_<ApiStatus>_)

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Print API status.

```APIDOC
## print(_<ApiStatus>_)

### Description
Print API status.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Call logging_info() function

Source: https://mrcieu.github.io/ieugwasr/reference/logging_info.html

This function is called for its side effects and does not return any value. Ensure it is called within the appropriate context for logging access token information.

```R
logging_info()
```

--------------------------------

### fill_n()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Look up sample sizes when meta data is missing from associations.

```APIDOC
## fill_n()

### Description
Look up sample sizes when meta data is missing from associations.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### LD Clumping with Local PLINK

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Perform LD clumping locally by providing a path to PLINK and a BED/BIM/FAM LD reference dataset.

```r
ld_clump(
    dplyr::tibble(rsid = a$rsid, pval = a$p, id = a$id),
    plink_bin = "/path/to/plink",
    bfile = "/path/to/reference_data"
)
```

--------------------------------

### Check Datasets in Upload Process

Source: https://mrcieu.github.io/ieugwasr/reference/editcheck.html

Use this function to check datasets that are currently being uploaded. It requires a dataset ID and optionally an authentication token.

```R
editcheck(id, opengwas_jwt = get_opengwas_jwt(), ...)
```

--------------------------------

### Get Specific Study Information

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Retrieve information for a particular GWAS study by its ID.

```r
gwasinfo("ieu-a-2")
```

--------------------------------

### Verify API Authentication

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Make a request to the API to retrieve user information, confirming your JWT token is valid and working.

```r
user()
```

--------------------------------

### api_query()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Wrapper for sending queries and payloads to API.

```APIDOC
## api_query()

### Description
Wrapper for sending queries and payloads to API.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### fill_n

Source: https://mrcieu.github.io/ieugwasr/reference/fill_n.html

Looks up sample sizes when meta data is missing from associations. It takes an output from `associations` as input and returns an updated version of it.

```APIDOC
## fill_n

### Description
Look up sample sizes when meta data is missing from associations.

### Usage
```R
fill_n(d, opengwas_jwt = get_opengwas_jwt(), ...)
```

### Arguments

*   `d` (Output from `associations`): The input data frame.
*   `opengwas_jwt` (string): Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
*   `...` (Unused): For extensibility.

### Value
Updated version of `d`.
```

--------------------------------

### api_query Function

Source: https://mrcieu.github.io/ieugwasr/reference/api_query.html

A generic function to access various GET and POST endpoints in the GWAS database API.

```APIDOC
## api_query

### Description
This function provides a generic way to access different GET and POST endpoints in the GWAS database API.

### Usage
```R
api_query(
  path,
  query = NULL,
  opengwas_jwt = get_opengwas_jwt(),
  method = "GET",
  silent = TRUE,
  encode = "json",
  timeout = 300,
  override_429 = FALSE,
  x_api_source = paste0("ieugwasr/", utils::packageVersion("ieugwasr"))
)
```

### Arguments

*   **path** (string) - Either a full query path (e.g. for get) or an endpoint (e.g. for post) queries.
*   **query** (list, optional) - If post query, provide a list of arguments as the payload. `NULL` by default.
*   **opengwas_jwt** (string, optional) - Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
*   **method** (string, optional) - Accepts `"GET"` (default), `"POST"`, `"DELETE"`, etc.
*   **silent** (boolean, optional) - `TRUE`/`FALSE` to be passed to httr call. `TRUE` by default.
*   **encode** (string, optional) - Default = `"json"`, see `httr::POST` for options.
*   **timeout** (numeric, optional) - Default = `300`. Avoid increasing this, preferentially simplify the query first.
*   **override_429** (boolean, optional) - Default=`FALSE`. If allowance is exceeded then the query will error before submitting a request to avoid getting blocked. If you are sure you want to submit the request then set this to TRUE.
*   **x_api_source** (string, optional) - Default = `paste0("ieugwasr/", utils::packageVersion("ieugwasr"))`.

### Value
httr response object
```

--------------------------------

### Get 1000 Genomes Annotations for HapMap3 Variants

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Extract 1000 Genomes annotations for the 1.3 million HapMap3 variants.

```r
afl2_list("hapmap3")
```

--------------------------------

### api_status()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

OpenGWAS server status.

```APIDOC
## api_status()

### Description
OpenGWAS server status.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get Variants by Gene

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Find variants within a particular gene region by providing an Ensembl or Entrez gene ID.

```r
c <- variants_gene("ENSG00000123374")
```

--------------------------------

### Select API Endpoint

Source: https://mrcieu.github.io/ieugwasr/reference/select_api.html

Use this function to switch between the public, private, or development API endpoints. The default is the public endpoint. Setting `silent = TRUE` will suppress messages about the API change.

```R
select_api(where = "public", silent = FALSE)
```

--------------------------------

### LD Clumping with API

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Perform LD clumping using the API with a default LD reference panel from 1000 genomes.

```r
a <- tophits(id = "ieu-a-2", clump = 0)
b <- ld_clump(
    dplyr::tibble(rsid = a$rsid, pval = a$p, id = a$id)
)
```

--------------------------------

### ld_clump_api()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Perform clumping on the chosen variants using through API.

```APIDOC
## ld_clump_api()

### Description
Perform clumping on the chosen variants using through API.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### check_access_token()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Check if authentication has been made.

```APIDOC
## check_access_token()

### Description
Check if authentication has been made.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get 1000 Genomes Annotations by rsID

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Look up population annotations, including alternative allele frequencies and LD scores, for a specific set of rsIDs from the 1000 Genomes project.

```r
afl2_rsid(c("rs234", "rs123"))
```

--------------------------------

### logging_info

Source: https://mrcieu.github.io/ieugwasr/reference/logging_info.html

This function logs information related to access tokens. It is called for its side effects and does not return any value.

```APIDOC
## logging_info()

### Description
Logs details about access token usage.

### Usage
```R
logging_info()
```

### Value
No return value, called for side effects.
```

--------------------------------

### gwasinfo_files

Source: https://mrcieu.github.io/ieugwasr/reference/gwasinfo_files.html

Returns a list of download URLs for each file (.vcf.gz, .vcf.gz.tbi, _report.html) associated with a dataset. The URLs will expire in 2 hours.

```APIDOC
## gwasinfo_files

### Description
Returns a list of download URLs for each file (.vcf.gz, .vcf.gz.tbi, _report.html) associated with a dataset. The URLs will expire in 2 hours. If a dataset is missing from the results, that means either the dataset doesn't exist or you don't have access to it. If a dataset is in the results but some/all links are missing, that means the files are unavailable.

### Method
`gwasinfo_files(id, opengwas_jwt = get_opengwas_jwt(), ...)`

### Parameters
#### Path Parameters
- **id** (List) - Required - List of OpenGWAS IDs to retrieve.

#### Query Parameters
- **opengwas_jwt** (string) - Optional - Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a JWT. Provide the JWT string here, or store in .Renviron under the keyname OPENGWAS_JWT.
- **...** - Unused, for extensibility

### Value
Dataframe of details for requested studies
```

--------------------------------

### Get Variant Info by Chromosome Position

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Retrieve variant information, including dbSNP IDs and gene info, by specifying chromosome and position. Accepts chr:position or chr:start-end formats.

```r
a <- variants_chrpos(c("7:105561135-105563135", "10:44865737"))
```

--------------------------------

### Perform LD clumping using local data

Source: https://mrcieu.github.io/ieugwasr/articles/local_ld.html

Performs LD clumping using local PLINK binaries and a specified LD reference panel. Requires a dataframe with 'rsid', 'pval', and 'trait_id' columns.

```R
ld_clump(
    dplyr::tibble(rsid = dat$rsid, pval = dat$pval, id = dat$trait_id),
    plink_bin = genetics.binaRies::get_plink_binary(),
    bfile = "/path/to/reference/EUR"
)
```

--------------------------------

### Print API Status Method

Source: https://mrcieu.github.io/ieugwasr/reference/print.ApiStatus.html

This is the S3 method for printing the API status. It takes an object of class 'ApiStatus' as input and prints its status. Unused arguments are included for extensibility.

```R
# S3 method for class 'ApiStatus'
print(x, ...)
```

--------------------------------

### General API Query (POST)

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Perform a POST request to an API endpoint, sending a list of query specifications in the payload. Useful for long lists of rsids.

```r
api_query("associations", query = list(rsid = c("rs234", "rs123"), id = c("ieu-a-2", "ieu-a-7")))
```

--------------------------------

### print.ApiStatus

Source: https://mrcieu.github.io/ieugwasr/reference/print.ApiStatus.html

This S3 method is used to print the status of the API, typically the output from the `api_status` function.

```APIDOC
## print.ApiStatus

### Description
Prints the status of the API. This is an S3 method for objects of class 'ApiStatus'.

### Usage
```R
# S3 method for class 'ApiStatus'
print(x, ...)
```

### Arguments
* `x` (Output from `api_status`): The object containing the API status information to be printed.
* `...` (Unused): Placeholder for future extensibility.

### Value
Prints the API status to the console.
```

--------------------------------

### legacy_ids()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Convert current IDs to legacy IDs.

```APIDOC
## legacy_ids()

### Description
Convert current IDs to legacy IDs.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### infer_ancestry()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies.

```APIDOC
## infer_ancestry()

### Description
Infer ancestry of GWAS dataset by matching against 1000 genomes allele frequencies.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get variants by chromosome and position

Source: https://mrcieu.github.io/ieugwasr/reference/variants_chrpos.html

Use this function to find all variants within a given radius of specified chromosome and positions. Input can be a list of chr:pos strings or ranges. Authentication may be required for protected endpoints.

```R
variants_chrpos(chrpos = c("3:46414943", "3:122991235"), radius = 100000)
```

--------------------------------

### Generate LD Matrix with Local PLINK

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Generate an LD matrix locally using PLINK and local LD reference data.

```r
ld_matrix(b$variant, plink_bin = "/path/to/plink", bfile = "/path/to/reference_data")
```

--------------------------------

### Get variants around a gene with default radius

Source: https://mrcieu.github.io/ieugwasr/reference/variants_gene.html

Retrieve variants around a gene using its Ensembl ID. The default radius is 0, meaning only variants directly overlapping the gene region will be returned unless a different radius is specified.

```r
variants_gene(gene = "ENSG00000123374")
```

--------------------------------

### print(_<GwasInfo>_)

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Print GWAS information.

```APIDOC
## print(_<GwasInfo>_)

### Description
Print GWAS information.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Get variants around a gene using Ensembl ID

Source: https://mrcieu.github.io/ieugwasr/reference/variants_gene.html

Use this function to retrieve variants within a specified radius of a gene. Provide the gene identifier (Ensembl or Entrez) and optionally a radius. Authentication may be required for certain endpoints.

```r
variants_gene(gene = "ENSG00000123374", radius = 50000)
```

--------------------------------

### Generate LD matrix using local data

Source: https://mrcieu.github.io/ieugwasr/articles/local_ld.html

Generates an LD r value matrix using local PLINK binaries and a specified LD reference panel. Accepts a vector of rsids.

```R
ieugwasr::ld_matrix(
    dat$rsid,
    plink_bin = genetics.binaRies::get_plink_binary(),
  bfile = "/path/to/reference/EUR"
)
```

--------------------------------

### Get variants around a gene using Entrez ID

Source: https://mrcieu.github.io/ieugwasr/reference/variants_gene.html

This function retrieves genetic variants near a gene. It accepts Entrez IDs for gene identification and allows specifying a search radius. Authentication can be handled via an opengwas_jwt argument or an environment variable.

```r
variants_gene(gene = 1017, radius = 50000)
```

--------------------------------

### ld_matrix_local

Source: https://mrcieu.github.io/ieugwasr/reference/ld_matrix_local.html

Calculates the LD matrix using local PLINK binary and a reference dataset.

```APIDOC
## ld_matrix_local

### Description
Calculates the LD matrix using local PLINK binary and a reference dataset.

### Usage
```R
ld_matrix_local(variants, bfile, plink_bin, with_alleles = TRUE)
```

### Arguments

*   **variants** (list) - Required - List of variants (rsids).
*   **bfile** (string) - Required - Path to bed/bim/fam ld reference panel.
*   **plink_bin** (string) - Optional - Specify path to plink binary. Default = `NULL`. See https://github.com/MRCIEU/genetics.binaRies for convenient access to plink binaries.
*   **with_alleles** (boolean) - Optional - Whether to append the allele names to the SNP names. Default: `TRUE`.

### Value

data frame
```

--------------------------------

### Retrieve Allele Frequency and LD Scores for Variant Lists

Source: https://mrcieu.github.io/ieugwasr/reference/afl2_list.html

Use this function to get ancestry-specific LD scores and allele frequencies for pre-defined lists of variants. Choose between a reduced set of common SNPs or the larger HapMap3 set. Authentication may be required for protected endpoints.

```R
afl2_list(variantlist = "reduced", opengwas_jwt = get_opengwas_jwt(), ...)
```

--------------------------------

### ld_clump_local Function

Source: https://mrcieu.github.io/ieugwasr/reference/ld_clump_local.html

Wrapper for clump function using local plink binary and ld reference dataset.

```APIDOC
## ld_clump_local

### Description
Wrapper for clump function using local plink binary and ld reference dataset.

### Usage
```R
ld_clump_local(dat, clump_kb, clump_r2, clump_p, bfile, plink_bin)
```

### Arguments 

*   **dat** (Dataframe) - Must have a variant name column (`variant`) and pval column called `pval`. If `id` is present then clumping will be done per unique id.
*   **clump_kb** (numeric) - Clumping kb window. Default is very strict, `10000`.
*   **clump_r2** (numeric) - Clumping r2 threshold. Default is very strict, `0.001`.
*   **clump_p** (numeric) - Clumping sig level for index variants. Default = `1` (i.e. no threshold).
*   **bfile** (string) - If this is provided then will use the API. Default = `NULL`.
*   **plink_bin** (string) - Specify path to plink binary. Default = `NULL`. See https://github.com/MRCIEU/genetics.binaRies for convenient access to plink binaries.

### Value
Data frame of clumped variants
```

--------------------------------

### get_query_content()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Parse out json response from httr object.

```APIDOC
## get_query_content()

### Description
Parse out json response from httr object.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### get_opengwas_jwt()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Retrieve OpenGWAS JSON Web Token from .Renviron file.

```APIDOC
## get_opengwas_jwt()

### Description
Retrieve OpenGWAS JSON Web Token from .Renviron file.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Perform LD clumping using API data

Source: https://mrcieu.github.io/ieugwasr/articles/local_ld.html

Performs LD clumping using the OpenGWAS API with default reference data. This is a simpler alternative when local operations are not required.

```R
a <- tophits(id="ieu-a-2", clump = 0)
b <- ld_clump(
    dplyr::tibble(rsid = a$rsid, pval = a$p, id = a$id)
)
```

--------------------------------

### editcheck()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Check datasets that are in process of being uploaded.

```APIDOC
## editcheck()

### Description
Check datasets that are in process of being uploaded.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### tophits()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Obtain top hits from a GWAS dataset.

```APIDOC
## tophits()

### Description
Obtain top hits from a GWAS dataset.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### afl2_list()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Retrieve allele frequency and LD scores for pre-defined lists of variants.

```APIDOC
## afl2_list()

### Description
Retrieve allele frequency and LD scores for pre-defined lists of variants.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Local LD Clumping Function Wrapper

Source: https://mrcieu.github.io/ieugwasr/reference/ld_clump_local.html

Use this function to perform LD clumping using a local PLINK binary and a specified LD reference dataset. Ensure your input dataframe contains 'variant' and 'pval' columns. The 'id' column can be used for per-ID clumping.

```R
ld_clump_local(dat, clump_kb, clump_r2, clump_p, bfile, plink_bin)
```

--------------------------------

### Authenticate with OpenGWAS API

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Check if your JWT token is recognized by the ieugwasr package. Ensure you have set the OPENGWAS_JWT environment variable.

```r
library(ieugwasr)
get_opengwas_jwt()
```

--------------------------------

### check_reset()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Check if OpenGWAS allowance needs to be reset.

```APIDOC
## check_reset()

### Description
Check if OpenGWAS allowance needs to be reset.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Check OpenGWAS Allowance Reset

Source: https://mrcieu.github.io/ieugwasr/reference/check_reset.html

Use this function to check if the OpenGWAS allowance has been used up. It will error if a new query is submitted before the reset time to prevent IP blocking. Set `override_429` to `TRUE` to bypass this check.

```r
check_reset(override_429 = FALSE)
```

--------------------------------

### set_reset()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Set the reset time for OpenGWAS allowance.

```APIDOC
## set_reset()

### Description
Set the reset time for OpenGWAS allowance.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Perform PheWAS in specific batches

Source: https://mrcieu.github.io/ieugwasr/articles/guide.html

Perform PheWAS in only specified batches using the 'batch' argument.

```r
phewas(variants = "rs1205", pval = 1e-5, batch = c('ieu-a', 'ukb-b'))
```

--------------------------------

### legacy_ids

Source: https://mrcieu.github.io/ieugwasr/reference/legacy_ids.html

Converts a vector of current IDs to their legacy ID equivalents.

```APIDOC
## legacy_ids

### Description
Converts a vector of current IDs to their legacy ID equivalents.

### Usage
```R
legacy_ids(x)
```

### Arguments
* `x` (vector) - A vector of IDs to be converted.

### Value
Returns a vector of back-compatible (legacy) IDs.
```

--------------------------------

### afl2_chrpos()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Look up allele frequencies and LD scores for 1000 genomes populations by chrpos.

```APIDOC
## afl2_chrpos()

### Description
Look up allele frequencies and LD scores for 1000 genomes populations by chrpos.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### get_query_content

Source: https://mrcieu.github.io/ieugwasr/reference/get_query_content.html

Parses the JSON response from an API query.

```APIDOC
## get_query_content

### Description
Parses out JSON response from an httr object.

### Usage
```R
get_query_content(response)
```

### Arguments
* `response` (httr object) - Output from `api_query()`

### Value
Parsed JSON output from query, often in the form of a data frame. If the status code is not successful, then the actual response is returned.
```

--------------------------------

### ld_clump()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Perform LD clumping on SNP data.

```APIDOC
## ld_clump()

### Description
Perform LD clumping on SNP data.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### editcheck Function

Source: https://mrcieu.github.io/ieugwasr/reference/editcheck.html

Checks datasets that are in process of being uploaded. It requires a dataset ID and an optional JWT for authentication.

```APIDOC
## editcheck

### Description
Check datasets that are in process of being uploaded.

### Usage
```R
editcheck(id, opengwas_jwt = get_opengwas_jwt(), ...)
```

### Arguments 

* **id** (string) - Required - The ID of the dataset to check.
* **opengwas_jwt** (string) - Optional - Used to authenticate protected endpoints. Login to https://api.opengwas.io to obtain a jwt. Provide the jwt string here, or store in .Renviron under the keyname OPENGWAS_JWT.
* **...** - Unused, for extensibility

### Value
Dataframe
```

--------------------------------

### associations()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Query specific variants from specific GWAS.

```APIDOC
## associations()

### Description
Query specific variants from specific GWAS.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### Check OpenGWAS Server Status

Source: https://mrcieu.github.io/ieugwasr/reference/api_status.html

Use the `api_status` function to retrieve a list of values regarding the status of OpenGWAS servers. This function is designed for extensibility and accepts additional arguments.

```R
api_status(...)
```

--------------------------------

### print.GwasInfo

Source: https://mrcieu.github.io/ieugwasr/reference/print.GwasInfo.html

This S3 method is used to print GWAS information that has been retrieved using the `gwasinfo` function.

```APIDOC
## print.GwasInfo

### Description
Prints GWAS information.

### Usage
```R
# S3 method for class 'GwasInfo'
print(x, ...)
```

### Arguments
* `x` (Output from `gwasinfo`): The GWAS information object to print.
* `...` (Unused): For extensibility.

### Value
Prints out GWAS information to the console.
```

--------------------------------

### Check Access Token Status

Source: https://mrcieu.github.io/ieugwasr/reference/check_access_token.html

This function is deprecated and should not be used. It was previously used to check if an access token was set. Use `get_opengwas_jwt()` for current authentication status.

```R
check_access_token()
```

--------------------------------

### batch_from_id()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Extract batch name from study ID.

```APIDOC
## batch_from_id()

### Description
Extract batch name from study ID.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### variants_rsid()

Source: https://mrcieu.github.io/ieugwasr/reference/index.html

Obtain information about rsid.

```APIDOC
## variants_rsid()

### Description
Obtain information about rsid.

### Method
N/A (Function Signature)

### Endpoint
N/A (Function Signature)

### Parameters
N/A (Function Signature)

### Request Example
N/A (Function Signature)

### Response
N/A (Function Signature)

### Response Example
N/A (Function Signature)
```

--------------------------------

### check_reset

Source: https://mrcieu.github.io/ieugwasr/reference/check_reset.html

Checks if the OpenGWAS allowance needs to be reset. It prevents the IP from being blocked by erroring if a new query is submitted before the reset time. If the allowance has been used up, it displays a message indicating the reset time. The default behavior is to throw an error if the allowance is used up, but this can be overridden.

```APIDOC
## Function: check_reset

### Description
Checks if a recent query indicated that the OpenGWAS allowance has been used up. To prevent the IP being blocked, it will error if the new query is being submitted before the reset time. If the allowance has been used up, it displays a message indicating the time when the allowance will be reset. By default, the function will throw an error if the allowance has been used up, but this behavior can be overridden by setting `override_429` to `TRUE`.

### Usage
```R
check_reset(override_429 = FALSE)
```

### Arguments

*   **override_429** (Logical) - Optional - Indicates whether to override the allowance reset check. Defaults to `FALSE`.
```