pandasgwas 0.99.10

A Python package for easy retrieval of GWAS catalog data

pandasGWAS: a Python package for easy retrieval of GWAS catalog data

Dependencies

python: 3.8
pandas: 1.4.3
requests: 2.28.1
progressbar2: 4.0.0

Documentation

See pandasGWAS Documentation

Development Environment

OS: Windows10 Professional
IDE: PyCharm 2022.1 (Community Edition)

Installation

pip install pandasgwas

Example

Get studies related to triple-negative breast cancer:

from pandasgwas.get_studies import get_studies
studies = get_studies(efo_trait = 'triple-negative breast cancer')
studies.studies[0:4]
#                  initialSampleSize                    gxe    gxg   snpCount  qualifier  imputed  pooled studyDesignComment  accessionId   fullPvalueSet  userRequested            platforms                                ancestries                                   genotypingTechnologies                             replicationSampleSize                                diseaseTrait.trait                 publicationInfo.pubmedId publicationInfo.publicationDate publicationInfo.publication               publicationInfo.title                publicationInfo.author.fullname publicationInfo.author.orcid
#0  1,529 European ancestry cases, 3,399 European ...  False  False        NaN    None     True     False        None           GCST002305      False          False      [{'manufacturer': 'Illumina'}]  [{'type': 'replication', 'numberOfIndividuals'...  [{'genotypingTechnology': 'Genome-wide genotyp...  2,148 European ancestry cases, 1,309 European ...  Breast cancer (estrogen-receptor negative, pro...         24325915                    2013-12-09                    Carcinogenesis      Genome-wide association study identifies 25 kn...           Purrington KS              0000-0002-5710-1692    
#1  8,602 European ancestry triple negative cases,...  False  False  9.700e+06       ~     True     False        None           GCST010100      False           True      [{'manufacturer': 'Illumina'}]  [{'type': 'initial', 'numberOfIndividuals': 11...  [{'genotypingTechnology': 'Genome-wide genotyp...                                                 NA  Breast cancer (estrogen-receptor negative, pro...         32424353                    2020-05-18                         Nat Genet      Genome-wide association study identifies 32 no...                 Zhang H                             None    
#2                5,631 European ancestry individuals  False  False  1.000e+07    None     True     False        None         GCST90029052      False          False                                  []  [{'type': 'initial', 'numberOfIndividuals': 56...  [{'genotypingTechnology': 'Genome-wide genotyp...                                                 NA  15-year breast cancer-specific survival (ER ne...         34407845                    2021-08-18                 Breast Cancer Res      Association of germline genetic variants with ...                 Morra A                             None

Find associated variants with study GCST002305:

from pandasgwas.get_SNPs import get_variants
variants = get_variants(study_id = 'GCST002305')
variants.single_nucleotide_polymorphisms[['rsId', 'functionalClass']]
#      rsId      functionalClass   
#0   rs4245739  3_prime_UTR_variant
#1   rs2363956     missense_variant
#2  rs10069690       intron_variant
#3   rs3757318       intron_variant
#4  rs10771399   intergenic_variant

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