Binds together GWAS Catalog objects of the same class. Note that bind() preserves duplicates whereas union does not.

bind(x, ...)

Arguments

x

An object of class: studies, associations, variants, or traits.

...

Objects of the same class as x.

Value

An object of the same class as x.

Examples

# Join two studies objects. bind(studies_ex01, studies_ex02)
#> An object of class "studies" #> Slot "studies": #> # A tibble: 4 x 13 #> study_id reported_trait initial_sample_… replication_sam… gxe gxg #> <chr> <chr> <chr> <chr> <lgl> <lgl> #> 1 GCST001… Breast size 16,175 European… NA FALSE FALSE #> 2 GCST003… Breast size 33,790 European… NA FALSE FALSE #> 3 GCST001… Breast size 16,175 European… NA FALSE FALSE #> 4 GCST006… Breast size 5,609 Japanese … NA FALSE FALSE #> # … with 7 more variables: snp_count <int>, qualifier <chr>, imputed <lgl>, #> # pooled <lgl>, study_design_comment <chr>, full_pvalue_set <lgl>, #> # user_requested <lgl> #> #> Slot "genotyping_techs": #> # A tibble: 4 x 2 #> study_id genotyping_technology #> <chr> <chr> #> 1 GCST001585 Genome-wide genotyping array #> 2 GCST003985 Genome-wide genotyping array #> 3 GCST001585 Genome-wide genotyping array #> 4 GCST006655 Genome-wide genotyping array #> #> Slot "platforms": #> # A tibble: 4 x 2 #> study_id manufacturer #> <chr> <chr> #> 1 GCST001585 Illumina #> 2 GCST003985 Illumina #> 3 GCST001585 Illumina #> 4 GCST006655 Affymetrix #> #> Slot "ancestries": #> # A tibble: 4 x 4 #> study_id ancestry_id type number_of_individuals #> <chr> <int> <chr> <int> #> 1 GCST001585 1 initial 16175 #> 2 GCST003985 1 initial 33790 #> 3 GCST001585 1 initial 16175 #> 4 GCST006655 1 initial 5609 #> #> Slot "ancestral_groups": #> # A tibble: 4 x 3 #> study_id ancestry_id ancestral_group #> <chr> <int> <chr> #> 1 GCST001585 1 European #> 2 GCST003985 1 European #> 3 GCST001585 1 European #> 4 GCST006655 1 East Asian #> #> Slot "countries_of_origin": #> # A tibble: 4 x 5 #> study_id ancestry_id country_name major_area region #> <chr> <int> <chr> <chr> <chr> #> 1 GCST001585 1 NA NA NA #> 2 GCST003985 1 NA NA NA #> 3 GCST001585 1 NA NA NA #> 4 GCST006655 1 NA NA NA #> #> Slot "countries_of_recruitment": #> # A tibble: 4 x 5 #> study_id ancestry_id country_name major_area region #> <chr> <int> <chr> <chr> <chr> #> 1 GCST001585 1 NA NA NA #> 2 GCST003985 1 NA NA NA #> 3 GCST001585 1 NA NA NA #> 4 GCST006655 1 NA NA NA #> #> Slot "publications": #> # A tibble: 4 x 7 #> study_id pubmed_id publication_date publication title author_fullname #> <chr> <int> <date> <chr> <chr> <chr> #> 1 GCST001… 22747683 2012-06-29 BMC Med Ge… Gene… Eriksson N #> 2 GCST003… 27182965 2016-05-15 Nat Genet Dete… Pickrell JK #> 3 GCST001… 22747683 2012-06-29 BMC Med Ge… Gene… Eriksson N #> 4 GCST006… 29855537 2018-05-30 Sci Rep Japa… Hirata T #> # … with 1 more variable: author_orcid <chr> #>
# Join two associations objects. bind(associations_ex01, associations_ex02)
#> An object of class "associations" #> Slot "associations": #> # A tibble: 7 x 17 #> association_id pvalue pvalue_descript… pvalue_mantissa pvalue_exponent #> <chr> <dbl> <chr> <int> <int> #> 1 22509 3.00e- 9 NA 3 -9 #> 2 22505 7.00e- 6 NA 7 -6 #> 3 19537565 7.00e-31 NA 7 -31 #> 4 19537593 1.00e-11 NA 1 -11 #> 5 19537593 1.00e-11 NA 1 -11 #> 6 31665940 8.00e- 6 NA 8 -6 #> 7 34944736 6.00e- 9 NA 6 -9 #> # … with 12 more variables: multiple_snp_haplotype <lgl>, #> # snp_interaction <lgl>, snp_type <chr>, standard_error <dbl>, range <chr>, #> # or_per_copy_number <dbl>, beta_number <dbl>, beta_unit <chr>, #> # beta_direction <chr>, beta_description <chr>, last_mapping_date <dttm>, #> # last_update_date <dttm> #> #> Slot "loci": #> # A tibble: 7 x 4 #> association_id locus_id haplotype_snp_count description #> <chr> <int> <int> <chr> #> 1 22509 1 NA Single variant #> 2 22505 1 NA Single variant #> 3 19537565 1 NA Single variant #> 4 19537593 1 NA Single variant #> 5 19537593 1 NA Single variant #> 6 31665940 1 NA Single variant #> 7 34944736 1 NA Single variant #> #> Slot "risk_alleles": #> # A tibble: 7 x 7 #> association_id locus_id variant_id risk_allele risk_frequency genome_wide #> <chr> <int> <chr> <chr> <dbl> <lgl> #> 1 22509 1 rs7089814 C NA NA #> 2 22505 1 chr22:458… T NA NA #> 3 19537565 1 rs10110651 NA NA FALSE #> 4 19537593 1 rs9397437 NA NA FALSE #> 5 19537593 1 rs9397437 NA NA FALSE #> 6 31665940 1 rs985648 G 0.248 FALSE #> 7 34944736 1 rs1469924… TTCTTTCTTTC 0.381 FALSE #> # … with 1 more variable: limited_list <lgl> #> #> Slot "genes": #> # A tibble: 13 x 3 #> association_id locus_id gene_name #> <chr> <int> <chr> #> 1 22509 1 ADO #> 2 22509 1 ZNF365 #> 3 22509 1 ALDH7A1P4 #> 4 22505 1 TBC1D22A #> 5 22505 1 LOC100128818 #> 6 19537565 1 KCNU1 #> 7 19537565 1 ZNF703 #> 8 19537593 1 CCDC170 #> 9 19537593 1 ESR1 #> 10 19537593 1 CCDC170 #> 11 19537593 1 ESR1 #> 12 31665940 1 NA #> 13 34944736 1 KCNU1 #> #> Slot "ensembl_ids": #> # A tibble: 13 x 4 #> association_id locus_id gene_name ensembl_id #> <chr> <int> <chr> <chr> #> 1 22509 1 ADO ENSG00000181915 #> 2 22509 1 ZNF365 ENSG00000138311 #> 3 22509 1 ALDH7A1P4 ENSG00000234489 #> 4 22505 1 TBC1D22A ENSG00000054611 #> 5 22505 1 LOC100128818 NA #> 6 19537565 1 KCNU1 ENSG00000215262 #> 7 19537565 1 ZNF703 ENSG00000183779 #> 8 19537593 1 CCDC170 ENSG00000120262 #> 9 19537593 1 ESR1 ENSG00000091831 #> 10 19537593 1 CCDC170 ENSG00000120262 #> 11 19537593 1 ESR1 ENSG00000091831 #> 12 31665940 1 NA NA #> 13 34944736 1 KCNU1 ENSG00000215262 #> #> Slot "entrez_ids": #> # A tibble: 13 x 4 #> association_id locus_id gene_name entrez_id #> <chr> <int> <chr> <chr> #> 1 22509 1 ADO 84890 #> 2 22509 1 ZNF365 22891 #> 3 22509 1 ALDH7A1P4 544 #> 4 22505 1 TBC1D22A 25771 #> 5 22505 1 LOC100128818 NA #> 6 19537565 1 KCNU1 157855 #> 7 19537565 1 ZNF703 80139 #> 8 19537593 1 CCDC170 80129 #> 9 19537593 1 ESR1 2099 #> 10 19537593 1 CCDC170 80129 #> 11 19537593 1 ESR1 2099 #> 12 31665940 1 NA NA #> 13 34944736 1 KCNU1 157855 #>
# Join two variants objects. bind(variants_ex01, variants_ex02)
#> An object of class "variants" #> Slot "variants": #> # A tibble: 7 x 7 #> variant_id merged functional_class chromosome_name chromosome_posi… #> <chr> <int> <chr> <chr> <int> #> 1 rs1469924… 0 regulatory_regi… 8 36984538 #> 2 rs56261590 0 intron_variant 4 73189781 #> 3 rs4725504 0 intergenic_vari… 7 153608338 #> 4 rs56261590 0 intron_variant 4 73189781 #> 5 rs4725504 0 intergenic_vari… 7 153608338 #> 6 rs11099757 0 intron_variant 4 150143216 #> 7 rs16871509 0 intergenic_vari… 5 71726395 #> # … with 2 more variables: chromosome_region <chr>, last_update_date <dttm> #> #> Slot "genomic_contexts": #> # A tibble: 44 x 11 #> variant_id gene_name chromosome_name chromosome_posi… distance #> <chr> <chr> <chr> <int> <int> #> 1 rs1469924… LOC10537… 8 36984538 81555 #> 2 rs1469924… KCNU1 8 36984538 48413 #> 3 rs1469924… LOC10537… 8 36984538 2533 #> 4 rs1469924… TPT1P8 8 36984538 95231 #> 5 rs1469924… RPL26P25 8 36984538 3392 #> 6 rs1469924… KCNU1 8 36984538 48413 #> 7 rs1469924… AC090453… 8 36984538 3439 #> 8 rs1469924… TPT1P8 8 36984538 95008 #> 9 rs1469924… AC092818… 8 36984538 82903 #> 10 rs1469924… LOC10537… 8 36984538 59331 #> # … with 34 more rows, and 6 more variables: is_closest_gene <lgl>, #> # is_intergenic <lgl>, is_upstream <lgl>, is_downstream <lgl>, source <chr>, #> # mapping_method <chr> #> #> Slot "ensembl_ids": #> # A tibble: 23 x 3 #> variant_id gene_name ensembl_id #> <chr> <chr> <chr> #> 1 rs146992477 KCNU1 ENSG00000215262 #> 2 rs146992477 TPT1P8 ENSG00000219491 #> 3 rs146992477 AC090453.1 ENSG00000243503 #> 4 rs146992477 AC092818.1 ENSG00000254038 #> 5 rs56261590 ANKRD17 ENSG00000132466 #> 6 rs56261590 HMGA1P2 ENSG00000248641 #> 7 rs56261590 AC053527.1 ENSG00000250220 #> 8 rs56261590 RF00334 ENSG00000221093 #> 9 rs4725504 DPP6 ENSG00000130226 #> 10 rs4725504 PAXBP1P1 ENSG00000233489 #> # … with 13 more rows #> #> Slot "entrez_ids": #> # A tibble: 24 x 3 #> variant_id gene_name entrez_id #> <chr> <chr> <chr> #> 1 rs146992477 LOC105379377 105379377 #> 2 rs146992477 KCNU1 157855 #> 3 rs146992477 LOC105379376 105379376 #> 4 rs146992477 TPT1P8 59347 #> 5 rs146992477 RPL26P25 100270966 #> 6 rs146992477 LOC105379375 105379375 #> 7 rs56261590 ANKRD17 26057 #> 8 rs56261590 HMGA1P2 171559 #> 9 rs56261590 LOC102724832 102724832 #> 10 rs4725504 DPP6 1804 #> # … with 14 more rows #>
# Join two traits objects. bind(traits_ex01, traits_ex02)
#> An object of class "traits" #> Slot "traits": #> # A tibble: 7 x 3 #> efo_id trait uri #> <chr> <chr> <chr> #> 1 EFO_0004884 breast size http://www.ebi.ac.uk/efo/EFO_0004884 #> 2 EFO_0004343 waist-hip ratio http://www.ebi.ac.uk/efo/EFO_0004343 #> 3 EFO_0005299 non-word reading http://www.ebi.ac.uk/efo/EFO_0005299 #> 4 EFO_0007845 lip morphology measurement http://www.ebi.ac.uk/efo/EFO_0007845 #> 5 EFO_0004699 gambling http://www.ebi.ac.uk/efo/EFO_0004699 #> 6 EFO_0004884 breast size http://www.ebi.ac.uk/efo/EFO_0004884 #> 7 EFO_0004875 mathematical ability http://www.ebi.ac.uk/efo/EFO_0004875 #>