Package 'ieugwasr'

Title: Interface to the 'OpenGWAS' Database API
Description: Interface to the 'OpenGWAS' database API <https://api.opengwas.io/api/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.
Authors: Gibran Hemani [aut, cre, cph] , Ben Elsworth [aut] , Tom Palmer [aut] , Rita Rasteiro [aut]
Maintainer: Gibran Hemani <[email protected]>
License: MIT + file LICENSE
Version: 1.0.2
Built: 2024-11-20 05:20:57 UTC
Source: https://github.com/MRCIEU/ieugwasr

Help Index

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

Description

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

Usage

afl2_chrpos(chrpos, reference = "1000g", opengwas_jwt = get_opengwas_jwt())

Arguments

chrpos

list of ⁠<chr>:<pos>⁠ in build 37, e.g. c("3:46414943", "3:122991235"). Also allows ranges e.g "7:105561135-105563135"
reference

Default="1000g"
opengwas_jwt

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.

Value

Data frame containing ancestry specific LD scores and allele frequencies for each variant

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

Description

Data frame includes 1000 genomes metadata including sample sizes, allele frequency and LD score, separated by 5 super populations (EUR = European, AFR = African, EAS = East Asian, AMR = Admixed American, SAS = South Asian)

Usage

afl2_list(
  variantlist = c("reduced", "hapmap3")[1],
  opengwas_jwt = get_opengwas_jwt()
)

Arguments

variantlist

Choose pre-defined list. reduced = ~20k SNPs that are common in all super populations (default). hapmap3 = ~1.3 million hm3 SNPs
opengwas_jwt

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.

Value

Data frame containing ancestry specific LD scores and allele frequencies for each variant

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

Description

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

Usage

afl2_rsid(rsid, reference = "1000g", opengwas_jwt = get_opengwas_jwt())

Arguments

rsid

Vector of rsids
reference

Default="1000g"
opengwas_jwt

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.

Value

Data frame containing ancestry specific LD scores and allele frequencies for each variant

Wrapper for sending queries and payloads to API

Description

There are a number of different GET and POST endpoints in the GWAS database API. This is a generic way to access them.

Usage

api_query(
  path,
  query = NULL,
  opengwas_jwt = get_opengwas_jwt(),
  method = "GET",
  silent = TRUE,
  encode = "json",
  timeout = 300,
  override_429 = FALSE
)

Arguments

path

Either a full query path (e.g. for get) or an endpoint (e.g. for post) queries
query

If post query, provide a list of arguments as the payload. NULL by default
opengwas_jwt

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

"GET" (default) or "POST", "DELETE" etc
silent

TRUE/FALSE to be passed to httr call. TRUE by default
encode

Default = "json", see httr::POST for options
timeout

Default = 300, avoid increasing this, preferentially simplify the query first.
override_429

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.

Value

httr response object

MR-Base server status

Description

MR-Base server status

Usage

api_status()

Value

list of values regarding status

Query specific variants from specific GWAS

Description

Every rsid is searched for against each requested GWAS id. To get a list of available GWAS ids, or to find their meta data, use gwasinfo. Can request LD proxies for instances when the requested rsid is not present in a particular GWAS dataset. This currently only uses an LD reference panel composed of Europeans in 1000 genomes version 3. It is also restricted to biallelic single nucleotide polymorphisms (no indels), with European MAF > 0.01.

Usage

associations(
  variants,
  id,
  proxies = 1,
  r2 = 0.8,
  align_alleles = 1,
  palindromes = 1,
  maf_threshold = 0.3,
  opengwas_jwt = get_opengwas_jwt()
)

Arguments

variants

Array of variants e.g. c("rs234", "7:105561135-105563135")
id

Array of GWAS studies to query. See gwasinfo for available studies
proxies

0 or (default) 1 - indicating whether to look for proxies
r2

Minimum proxy LD rsq value. Default=0.8
align_alleles

Try to align tag alleles to target alleles (if proxies = 1). 1 = yes (default), 0 = no
palindromes

Allow palindromic SNPs (if proxies = 1). 1 = yes (default), 0 = no
maf_threshold

MAF threshold to try to infer palindromic SNPs. Default = 0.3.
opengwas_jwt

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.

Value

Dataframe

Extract batch name from study ID

Description

Extract batch name from study ID

Usage

batch_from_id(id)

Arguments

id

Array of study IDs

Value

Array of batch names

Get list of data batches in IEU GWAS database

Description

Get list of data batches in IEU GWAS database

Usage

batches(opengwas_jwt = get_opengwas_jwt())

Arguments

opengwas_jwt

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.

Value

data frame

Check if authentication has been maded

Description

Deprectated. Use get_opengwas_jwt() instead. See https://mrcieu.github.io/ieugwasr/articles/guide.html#authentication for more information.

Usage

check_access_token()

Value

NULL or access_token depending on current authentication state

Check if OpenGWAS allowance needs to be reset

Description

This function 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

check_reset(override_429 = FALSE)

Arguments

override_429

Logical value indicating whether to override the allowance reset check (default: FALSE)

Check datasets that are in process of being uploaded

Description

Check datasets that are in process of being uploaded

Usage

editcheck(id, opengwas_jwt = get_opengwas_jwt())

Arguments

id

ID
opengwas_jwt

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.

Value

Dataframe

Look up sample sizes when meta data is missing from associations

Description

Look up sample sizes when meta data is missing from associations

Usage

fill_n(d, opengwas_jwt = get_opengwas_jwt())

Arguments

d

Output from associations
opengwas_jwt

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.

Value

Updated version of d

Retrieve OpenGWAS JSON Web Token from .Renviron file

Description

Retrieve OpenGWAS JSON Web Token from .Renviron file

Usage

get_opengwas_jwt()

Value

JWT string

Parse out json response from httr object

Description

Parse out json response from httr object

Usage

get_query_content(response)

Arguments

response

Output from httr

Value

Parsed json output from query, often in form of data frame. If status code is not successful then return the actual response

Get list of studies with available GWAS summary statistics through API

Description

Get list of studies with available GWAS summary statistics through API

Usage

gwasinfo(id = NULL, opengwas_jwt = get_opengwas_jwt())

Arguments

id

List of MR-Base IDs to retrieve. If NULL (default) retrieves all available datasets
opengwas_jwt

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.

Value

Dataframe of details for all available studies

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

Description

Uses ~20k SNPs selected for common frequency across 5 major super populations

Usage

infer_ancestry(d, snpinfo = NULL, opengwas_jwt = get_opengwas_jwt())

Arguments

d

Data frame containing at least rsid and eaf columns. e.g. output from associations
snpinfo

Output from afl2_list, afl2_rsid or afl2_chrpos. If NULL then afl2_list() is used by default
opengwas_jwt

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.

Value

data frame ordered by most likely ancestry, each row represents a super population and cor column represents the correlation between the GWAS dataset and the 1000 genomes super population allele frequencies

Perform LD clumping on SNP data

Description

Uses PLINK clumping method, where SNPs in LD within a particular window will be pruned. The SNP with the lowest p-value is retained.

Usage

ld_clump(
  dat = NULL,
  clump_kb = 10000,
  clump_r2 = 0.001,
  clump_p = 0.99,
  pop = "EUR",
  opengwas_jwt = get_opengwas_jwt(),
  bfile = NULL,
  plink_bin = NULL
)

Arguments

dat

Dataframe. Must have a variant name column (rsid) and pval column called pval. If id is present then clumping will be done per unique id.
clump_kb

Clumping kb window. Default is very strict, 10000
clump_r2

Clumping r2 threshold. Default is very strict, 0.001
clump_p

Clumping sig level for index variants. Default = 1 (i.e. no threshold)
pop

Super-population to use as reference panel. Default = "EUR". Options are "EUR", "SAS", "EAS", "AFR", "AMR". 'legacy' also available - which is a previously used verison of the EUR panel with a slightly different set of markers
opengwas_jwt

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.#'
bfile

If this is provided then will use the API. Default = NULL
plink_bin

If NULL and bfile is not NULL then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = NULL

Details

This function interacts with the OpenGWAS API, which houses LD reference panels for the 5 super-populations in the 1000 genomes reference panel. It includes only bi-allelic SNPs with MAF > 0.01, so it's quite possible that a variant you want to include in the clumping process will be absent. If it is absent, it will be automatically excluded from the results.

You can check if your variants are present in the LD reference panel using ld_reflookup().

This function does put load on the OpenGWAS servers, which makes life more difficult for other users. We have implemented a method and made available the LD reference panels to perform clumping locally, see ld_clump() and related vignettes for details.

Value

Data frame

Perform clumping on the chosen variants using through API

Description

Perform clumping on the chosen variants using through API

Usage

ld_clump_api(
  dat,
  clump_kb = 10000,
  clump_r2 = 0.1,
  clump_p,
  pop = "EUR",
  opengwas_jwt = get_opengwas_jwt()
)

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

Clumping kb window. Default is very strict, 10000
clump_r2

Clumping r2 threshold. Default is very strict, 0.001
clump_p

Clumping sig level for index variants. Default = 1 (i.e. no threshold)
pop

Super-population to use as reference panel. Default = "EUR". Options are "EUR", "SAS", "EAS", "AFR", "AMR"
opengwas_jwt

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.#' @param bfile If this is provided then will use the API. Default = NULL

Value

Data frame of only independent variants

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

Description

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

Usage

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

Clumping kb window. Default is very strict, 10000
clump_r2

Clumping r2 threshold. Default is very strict, 0.001
clump_p

Clumping sig level for index variants. Default = 1 (i.e. no threshold)
bfile

If this is provided then will use the API. Default = NULL
plink_bin

Specify path to plink binary. Default = NULL. See https://github.com/explodecomputer/plinkbinr for convenient access to plink binaries

Value

data frame of clumped variants

Get LD matrix for list of SNPs

Description

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.

Usage

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

Arguments

variants

List of variants (rsids)
with_alleles

Whether to append the allele names to the SNP names. Default: TRUE
pop

Super-population to use as reference panel. Default = "EUR". Options are "EUR", "SAS", "EAS", "AFR", "AMR". 'legacy' also available - which is a previously used verison of the EUR panel with a slightly different set of markers
opengwas_jwt

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.#' @param bfile If this is provided then will use the API. Default = NULL
bfile

If this is provided then will use the API. Default = NULL
plink_bin

If NULL and bfile is not NULL then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = NULL

Details

The data used for generating the LD matrix includes only bi-allelic SNPs with MAF > 0.01, so it's quite possible that a variant you want to include will be absent. If it is absent, it will be automatically excluded from the results.

You can check if your variants are present in the LD reference panel using ld_reflookup()

This function does put load on the OpenGWAS servers, which makes life more difficult for other users, and has been limited to analyse only up to 500 variants at a time. We have implemented a method and made available the LD reference panels to perform the operation locally, see ld_matrix() and related vignettes for details.

Value

Matrix of LD r values

Get LD matrix using local plink binary and reference dataset

Description

Get LD matrix using local plink binary and reference dataset

Usage

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

Arguments

variants

List of variants (rsids)
bfile

Path to bed/bim/fam ld reference panel
plink_bin

Specify path to plink binary. Default = NULL. See https://github.com/explodecomputer/plinkbinr for convenient access to plink binaries
with_alleles

Whether to append the allele names to the SNP names. Default: TRUE

Value

data frame

Check which rsids are present in a remote LD reference panel

Description

Provide a list of rsids that you may want to perform LD operations on to check if they are present in the LD reference panel. If they are not then some functions e.g. ld_clump will exclude them from the analysis, so you may want to consider how to handle those variants in your data.

Usage

ld_reflookup(rsid, pop = "EUR", opengwas_jwt = get_opengwas_jwt())

Arguments

rsid

Array of rsids to check
pop

Super-population to use as reference panel. Default = "EUR". Options are "EUR", "SAS", "EAS", "AFR", "AMR"
opengwas_jwt

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.#' @param bfile If this is provided then will use the API. Default = NULL

Value

Array of rsids that are present in the LD reference panel

Convert current IDs to legacy IDs

Description

Convert current IDs to legacy IDs

Usage

legacy_ids(x)

Arguments

x

Vector of ids

Value

vector of back compatible ids

Details of how access token logs are used

Description

Details of how access token logs are used

Usage

logging_info()

Value

No return value, called for side effects

Perform fast phewas of a specific variants against all available GWAS datasets

Description

This is faster than doing it manually through associations

Usage

phewas(variants, pval = 1e-05, batch = c(), opengwas_jwt = get_opengwas_jwt())

Arguments

variants

Array of variants e.g. c("rs234", "7:105561135-105563135")
pval

p-value threshold. Default = 0.00001
batch

Vector of batch IDs to search across. If c() (default) then returns all batches
opengwas_jwt

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.

Value

Dataframe

Print API status

Description

Print API status

Usage

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

Arguments

x

Output from api_status
...

Unused, for extensibility

Value

Print out of API status

Print GWAS information

Description

Print GWAS information

Usage

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

Arguments

x

Output from gwasinfo
...

Unused, for extensibility

Value

Print out of GWAS information

Toggle API address between development and release

Description

Toggle API address between development and release

Usage

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

Arguments

where

Which API to use. Choice between "public", "private", "dev1", "dev2". Default = "public".
silent

Silent? Default = FALSE

Value

No return value, called for side effects

Set the reset time for OpenGWAS allowance

Description

This function sets the reset time for the OpenGWAS allowance based on the retry-after header returned by the API response. It also displays a warning message indicating the time at which the allowance will reset.

Usage

set_reset(r)

Arguments

r

The API response object

Value

None

Obtain top hits from a GWAS dataset

Description

By default performs clumping on the server side.

Usage

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

Arguments

id

Array of GWAS studies to query. See gwasinfo for available studies
pval

use this p-value threshold. Default = 5e-8
clump

whether to clump (1) or not (0). Default = 1
r2

use this clumping r2 threshold. Default is very strict, 0.001
kb

use this clumping kb window. Default is very strict, 10000
pop

Super-population to use as reference panel. Default = "EUR". Options are "EUR", "SAS", "EAS", "AFR", "AMR"
force_server

Logical. By default will return preclumped hits. p-value threshold 5e-8, with r2 threshold 0.001 and kb threshold 10000, using only SNPs with MAF > 0.01 in the European samples in 1000 genomes. If force_server = TRUE then will recompute using server side LD reference panel.
opengwas_jwt

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.

Value

Dataframe

Get user details

Description

Get user details

Usage

user(opengwas_jwt = get_opengwas_jwt())

Arguments

opengwas_jwt

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.

Value

user information

Obtain information about chr pos and surrounding region

Description

For a list of chromosome and positions, finds all variants within a given radius

Usage

variants_chrpos(chrpos, radius = 0, opengwas_jwt = get_opengwas_jwt())

Arguments

chrpos

list of ⁠<chr>:<pos>⁠ in build 37, e.g. c("3:46414943", "3:122991235"). Also allows ranges e.g. "7:105561135-105563135"
radius

Radius around each chrpos, default = 0
opengwas_jwt

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.

Value

Data frame

Obtain variants around a gene

Description

Provide a gene identified, either Ensembl or Entrez

Usage

variants_gene(gene, radius = 0, opengwas_jwt = get_opengwas_jwt())

Arguments

gene

Vector of genes, either Ensembl or Entrez, e.g. c("ENSG00000123374", "ENSG00000160791") or 1017
radius

Radius around the gene region to include. Default = 0
opengwas_jwt

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.

Value

data frame with the following columns

Obtain information about rsid

Description

Obtain information about rsid

Usage

variants_rsid(rsid, opengwas_jwt = get_opengwas_jwt())

Arguments

rsid

Vector of rsids
opengwas_jwt

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.

Value

data frame

Convert mixed array of rsid and chrpos to list of rsid

Description

Convert mixed array of rsid and chrpos to list of rsid

Usage

variants_to_rsid(variants, opengwas_jwt = get_opengwas_jwt())

Arguments

variants

Array of variants e.g. c("rs234", "7:105561135-105563135")
opengwas_jwt

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.

Value

list of rsids