Module ieugwaspy.query

API query functions

Functions

def associations(variant, id, proxies=1, r2=0.8, align_alleles=1, palindromes=1, maf_threshold=0.3)
Expand source code 
def associations(
        variant,
        id,
        proxies=1,
        r2=0.8,
        align_alleles=1,
        palindromes=1,
        maf_threshold=0.3
):
    """Retrieve associations for specific SNP/study combinations

    Args:
        variant (list): list of variants, e.g. ["rs1205", "7:105561135", "7:105561135-105563135"]
        id (list): list of OpenGWAS IDs, e.g. ["ieu-a-1239", "ieu-a-2"]
        proxies (int): `1` or `0`, whether to look for proxies (1, default) or not (0)
        r2 (float): minimum proxy LD rsq value. Default = 0.8
        align_alleles (int): `1` or `0`, whether to try to align tag alleles to target alleles (1, default) or not (0). Only active when proxies = 1
        palindromes (int): `1` or `0`, whether to allow palindromic SNPs (1, default) or not (0). Only active when proxies = 1
        maf_threshold (float): MAF threshold to try to infer palindromic SNPs. Default = 0.3

    Returns:
        result: JSON object as returned by API

    """
    return _api_query("associations", method="POST", data={
        "variant": variant,
        "id": backwards.legacy_ids(id),
        "proxies": proxies,
        "r2": r2,
        "align_alleles": align_alleles,
        "palindromes": palindromes,
        "maf_threshold": maf_threshold
    })

Retrieve associations for specific SNP/study combinations

Args

variant : list
list of variants, e.g. ["rs1205", "7:105561135", "7:105561135-105563135"]
id : list
list of OpenGWAS IDs, e.g. ["ieu-a-1239", "ieu-a-2"]
proxies : int
1 or 0, whether to look for proxies (1, default) or not (0)
r2 : float
minimum proxy LD rsq value. Default = 0.8
align_alleles : int
1 or 0, whether to try to align tag alleles to target alleles (1, default) or not (0). Only active when proxies = 1
palindromes : int
1 or 0, whether to allow palindromic SNPs (1, default) or not (0). Only active when proxies = 1
maf_threshold : float
MAF threshold to try to infer palindromic SNPs. Default = 0.3

Returns

result
JSON object as returned by API
def gwasinfo(id=[])
Expand source code 
def gwasinfo(id=[]):
    """This function will return GWAS study meta-data describing the specific studies selected by id

    Args:
        id (list): OpenGWAS IDs of specific studies, e.g. ["ieu-a-1239", "ieu-a-2"]

    Returns:
        result: JSON object as returned by API

    """
    if id != []:
        return _api_query("gwasinfo", method="POST", data={
            "id": backwards.legacy_ids(id)
        })
    else:
        return _api_query("gwasinfo")

This function will return GWAS study meta-data describing the specific studies selected by id

Args

id : list
OpenGWAS IDs of specific studies, e.g. ["ieu-a-1239", "ieu-a-2"]

Returns

result
JSON object as returned by API
def gwasinfo_files(id)
Expand source code 
def gwasinfo_files(id):
    """This function will return temporary links to files available for the specific studies selected by id

    Args:
        id (list): OpenGWAS IDs of specific studies, e.g. ["ieu-a-1239", "ieu-a-2"]

    Returns:
        result: JSON object as returned by API

    """
    return _api_query("gwasinfo/files", method="POST", data={
        "id": backwards.legacy_ids(id)
    })

This function will return temporary links to files available for the specific studies selected by id

Args

id : list
OpenGWAS IDs of specific studies, e.g. ["ieu-a-1239", "ieu-a-2"]

Returns

result
JSON object as returned by API
def phewas(variant, pval=0.001, batch=[])
Expand source code 
def phewas(variant, pval=1e-3, batch=[]):
    """Perform phenome-wide association analysis (PheWAS) of variant(s) across all traits in the IEU GWAS database

    Args:
        variant (list): list of variants, e.g. ["rs1205", "7:105561135", "7:105561135-105563135"]
        pval (float): p-value threshold
        batch (list): OpenGWAS data batches, e.g. ["ieu-a"]. Leave empty to search across all batches

    Returns:
        result: JSON object as returned by API

    """
    rsid = ",".join(variants.variants_to_rsid(variant))
    return _api_query("phewas", method="POST", data={
        "variant": rsid,
        "pval": pval,
        "index_list": batch
    })

Perform phenome-wide association analysis (PheWAS) of variant(s) across all traits in the IEU GWAS database

Args

variant : list
list of variants, e.g. ["rs1205", "7:105561135", "7:105561135-105563135"]
pval : float
p-value threshold
batch : list
OpenGWAS data batches, e.g. ["ieu-a"]. Leave empty to search across all batches

Returns

result
JSON object as returned by API
def status()
Expand source code 
def status():
    """Check API status

    Returns:
        result: JSON object as returned by API

    """
    return _api_query("status")

Check API status

Returns

result
JSON object as returned by API
def tophits(id,
pval=5e-08,
preclumped=1,
clump=1,
bychr=0,
r2=0.001,
kb=10000,
pop='EUR',
force_server=False)
Expand source code 
def tophits(
        id,
        pval=5e-8,
        preclumped=1,
        clump=1,
        bychr=0,
        r2=0.001,
        kb=10000,
        pop="EUR",
        force_server=False
):
    """Retrieve association data for specific SNP/study combinations 

    Args:
        id (list): list of OpenGWAS IDs, e.g. ["ieu-a-1239", "ieu-a-2"]
        pval (float): use this p-value threshold. Default = 5e-8
        preclumped (int): `1` or `0`, whether to use pre-clumped hits (1, default) or not (0)
        clump (int): `1` or `0`, whether to clump (1, default) or not (0)
        bychr (int): `0` or `1`, whether to extract all at once (0, default) or by chromosome (1). There is a limit on query results so bychr might be required for some well-powered datasets
        r2 (float): use this clumping r2 threshold. Default = 0.001 (very strict)
        kb (int): use this clumping kb window. Default = 10000 (very strict)
        pop (str): `EUR`, `SAS`, `EAS`, `AFR`, `AMR` or `legacy`, indicating the population. Default = EUR
        force_server (bool): `True` or `False`. By False (default) it will return preclumped hits with pval = 5e-8, r2 = 0.001 and kb = 10000 and using only SNPs with MAF > 0.01 in the European (EUR) samples in 1000 genomes. If TRUE then it will recompute using server side LD reference panel

    Returns:
        result: JSON object as returned by API

    """
    if clump == 1 and pval == 5e-8 and r2 == 0.001 and kb == 10000:
        preclumped = 0 if force_server else 1
    else:
        preclumped = 0
    return _api_query("tophits", method="POST", data={
        "id": backwards.legacy_ids(id),
        "pval": pval,
        "preclumped": preclumped,
        "clump": clump,
        "bychr": bychr,
        "r2": r2,
        "kb": kb,
        "pop": pop
    })

Retrieve association data for specific SNP/study combinations

Args

id : list
list of OpenGWAS IDs, e.g. ["ieu-a-1239", "ieu-a-2"]
pval : float
use this p-value threshold. Default = 5e-8
preclumped : int
1 or 0, whether to use pre-clumped hits (1, default) or not (0)
clump : int
1 or 0, whether to clump (1, default) or not (0)
bychr : int
0 or 1, whether to extract all at once (0, default) or by chromosome (1). There is a limit on query results so bychr might be required for some well-powered datasets
r2 : float
use this clumping r2 threshold. Default = 0.001 (very strict)
kb : int
use this clumping kb window. Default = 10000 (very strict)
pop : str
EUR, SAS, EAS, AFR, AMR or legacy, indicating the population. Default = EUR
force_server : bool
True or False. By False (default) it will return preclumped hits with pval = 5e-8, r2 = 0.001 and kb = 10000 and using only SNPs with MAF > 0.01 in the European (EUR) samples in 1000 genomes. If TRUE then it will recompute using server side LD reference panel

Returns

result
JSON object as returned by API
def user()
Expand source code 
def user():
    """Get user information

    Returns:
        result: JSON object as returned by API

    """
    return _api_query("user")

Get user information

Returns

result
JSON object as returned by API