Performs set union, intersection, and (asymmetric!) difference on two objects of either class studies, associations, variants, or traits. Note that union() removes duplicated entities, whereas bind() does not.

union(x, y, ...)

intersect(x, y, ...)

setdiff(x, y, ...)

setequal(x, y, ...)

Arguments

x, y

Objects of either class studies, associations, variants, or traits.

...

other arguments passed on to methods.

Value

An object of the same class as x and y, i.e., studies, associations, variants, or traits.

Examples

# # union() # # Combine studies and remove duplicates union(studies_ex01, studies_ex02)
#> An object of class "studies" #> Slot "studies": #> # A tibble: 3 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 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: 3 x 2 #> study_id genotyping_technology #> <chr> <chr> #> 1 GCST001585 Genome-wide genotyping array #> 2 GCST003985 Genome-wide genotyping array #> 3 GCST006655 Genome-wide genotyping array #> #> Slot "platforms": #> # A tibble: 3 x 2 #> study_id manufacturer #> <chr> <chr> #> 1 GCST001585 Illumina #> 2 GCST003985 Illumina #> 3 GCST006655 Affymetrix #> #> Slot "ancestries": #> # A tibble: 3 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 GCST006655 1 initial 5609 #> #> Slot "ancestral_groups": #> # A tibble: 3 x 3 #> study_id ancestry_id ancestral_group #> <chr> <int> <chr> #> 1 GCST001585 1 European #> 2 GCST003985 1 European #> 3 GCST006655 1 East Asian #> #> Slot "countries_of_origin": #> # A tibble: 3 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 GCST006655 1 <NA> <NA> <NA> #> #> Slot "countries_of_recruitment": #> # A tibble: 3 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 GCST006655 1 <NA> <NA> <NA> #> #> Slot "publications": #> # A tibble: 3 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 GCST006… 29855537 2018-05-30 Sci Rep Japa… Hirata T #> # … with 1 more variable: author_orcid <chr> #>
# Combine associations and remove duplicates union(associations_ex01, associations_ex02)
#> An object of class "associations" #> Slot "associations": #> # A tibble: 6 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 31665940 8.00e- 6 <NA> 8 -6 #> 6 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: 6 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 31665940 1 NA Single variant #> 6 34944736 1 NA Single variant #> #> Slot "risk_alleles": #> # A tibble: 6 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 31665940 1 rs985648 G 0.248 FALSE #> 6 34944736 1 rs1469924… TTCTTTCTTTC 0.381 FALSE #> # … with 1 more variable: limited_list <lgl> #> #> Slot "genes": #> # A tibble: 11 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 31665940 1 <NA> #> 11 34944736 1 KCNU1 #> #> Slot "ensembl_ids": #> # A tibble: 11 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 31665940 1 <NA> <NA> #> 11 34944736 1 KCNU1 ENSG00000215262 #> #> Slot "entrez_ids": #> # A tibble: 11 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 31665940 1 <NA> <NA> #> 11 34944736 1 KCNU1 157855 #>
# Combine variants and remove duplicates union(variants_ex01, variants_ex02)
#> An object of class "variants" #> Slot "variants": #> # A tibble: 5 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 rs11099757 0 intron_variant 4 150143216 #> 5 rs16871509 0 intergenic_vari… 5 71726395 #> # … with 2 more variables: chromosome_region <chr>, last_update_date <dttm> #> #> Slot "genomic_contexts": #> # A tibble: 33 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 23 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: 17 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 #> 11 rs11099757 RNU7-194P ENSG00000238721 #> 12 rs11099757 DCLK2 ENSG00000170390 #> 13 rs11099757 RNU6-1230P ENSG00000207121 #> 14 rs11099757 AC105343.1 ENSG00000250704 #> 15 rs16871509 AC143336.1 ENSG00000278824 #> 16 rs16871509 CARTPT ENSG00000164326 #> 17 rs16871509 MCCC2 ENSG00000131844 #> #> Slot "entrez_ids": #> # A tibble: 18 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 #> 11 rs4725504 PAXBP1P1 106481704 #> 12 rs4725504 LOC107986750 107986750 #> 13 rs11099757 RNU7-194P 106480834 #> 14 rs11099757 DCLK2 166614 #> 15 rs11099757 RNU6-1230P 106481944 #> 16 rs16871509 CARTPT 9607 #> 17 rs16871509 MCCC2 64087 #> 18 rs16871509 LOC100422013 100422013 #>
# Combine traits and remove duplicates union(traits_ex01, traits_ex02)
#> An object of class "traits" #> Slot "traits": #> # A tibble: 6 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_0004875 mathematical ability http://www.ebi.ac.uk/efo/EFO_0004875 #>
# # intersect() # # Intersect common studies intersect(studies_ex01, studies_ex02)
#> An object of class "studies" #> Slot "studies": #> # A tibble: 1 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 #> # … 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: 1 x 2 #> study_id genotyping_technology #> <chr> <chr> #> 1 GCST001585 Genome-wide genotyping array #> #> Slot "platforms": #> # A tibble: 1 x 2 #> study_id manufacturer #> <chr> <chr> #> 1 GCST001585 Illumina #> #> Slot "ancestries": #> # A tibble: 1 x 4 #> study_id ancestry_id type number_of_individuals #> <chr> <int> <chr> <int> #> 1 GCST001585 1 initial 16175 #> #> Slot "ancestral_groups": #> # A tibble: 1 x 3 #> study_id ancestry_id ancestral_group #> <chr> <int> <chr> #> 1 GCST001585 1 European #> #> Slot "countries_of_origin": #> # A tibble: 1 x 5 #> study_id ancestry_id country_name major_area region #> <chr> <int> <chr> <chr> <chr> #> 1 GCST001585 1 <NA> <NA> <NA> #> #> Slot "countries_of_recruitment": #> # A tibble: 1 x 5 #> study_id ancestry_id country_name major_area region #> <chr> <int> <chr> <chr> <chr> #> 1 GCST001585 1 <NA> <NA> <NA> #> #> Slot "publications": #> # A tibble: 1 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 #> # … with 1 more variable: author_orcid <chr> #>
# Intersect common associations intersect(associations_ex01, associations_ex02)
#> An object of class "associations" #> Slot "associations": #> # A tibble: 1 x 17 #> association_id pvalue pvalue_descript… pvalue_mantissa pvalue_exponent #> <chr> <dbl> <chr> <int> <int> #> 1 19537593 1.00e-11 <NA> 1 -11 #> # … 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: 1 x 4 #> association_id locus_id haplotype_snp_count description #> <chr> <int> <int> <chr> #> 1 19537593 1 NA Single variant #> #> Slot "risk_alleles": #> # A tibble: 1 x 7 #> association_id locus_id variant_id risk_allele risk_frequency genome_wide #> <chr> <int> <chr> <chr> <dbl> <lgl> #> 1 19537593 1 rs9397437 <NA> NA FALSE #> # … with 1 more variable: limited_list <lgl> #> #> Slot "genes": #> # A tibble: 2 x 3 #> association_id locus_id gene_name #> <chr> <int> <chr> #> 1 19537593 1 CCDC170 #> 2 19537593 1 ESR1 #> #> Slot "ensembl_ids": #> # A tibble: 2 x 4 #> association_id locus_id gene_name ensembl_id #> <chr> <int> <chr> <chr> #> 1 19537593 1 CCDC170 ENSG00000120262 #> 2 19537593 1 ESR1 ENSG00000091831 #> #> Slot "entrez_ids": #> # A tibble: 2 x 4 #> association_id locus_id gene_name entrez_id #> <chr> <int> <chr> <chr> #> 1 19537593 1 CCDC170 80129 #> 2 19537593 1 ESR1 2099 #>
# Intersect common variants intersect(variants_ex01, variants_ex02)
#> An object of class "variants" #> Slot "variants": #> # A tibble: 2 x 7 #> variant_id merged functional_class chromosome_name chromosome_posi… #> <chr> <int> <chr> <chr> <int> #> 1 rs56261590 0 intron_variant 4 73189781 #> 2 rs4725504 0 intergenic_vari… 7 153608338 #> # … with 2 more variables: chromosome_region <chr>, last_update_date <dttm> #> #> Slot "genomic_contexts": #> # A tibble: 11 x 11 #> variant_id gene_name chromosome_name chromosome_posi… distance #> <chr> <chr> <chr> <int> <int> #> 1 rs56261590 ANKRD17 4 73189781 0 #> 2 rs56261590 ANKRD17 4 73189781 0 #> 3 rs56261590 HMGA1P2 4 73189781 90636 #> 4 rs56261590 HMGA1P2 4 73189781 89275 #> 5 rs56261590 LOC10272… 4 73189781 69394 #> 6 rs56261590 AC053527… 4 73189781 69428 #> 7 rs56261590 RF00334 4 73189781 74179 #> 8 rs4725504 DPP6 7 153608338 278759 #> 9 rs4725504 DPP6 7 153608338 139795 #> 10 rs4725504 PAXBP1P1 7 153608338 158463 #> 11 rs4725504 LOC10798… 7 153608338 84107 #> # … with 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: 6 x 3 #> variant_id gene_name ensembl_id #> <chr> <chr> <chr> #> 1 rs56261590 ANKRD17 ENSG00000132466 #> 2 rs56261590 HMGA1P2 ENSG00000248641 #> 3 rs56261590 AC053527.1 ENSG00000250220 #> 4 rs56261590 RF00334 ENSG00000221093 #> 5 rs4725504 DPP6 ENSG00000130226 #> 6 rs4725504 PAXBP1P1 ENSG00000233489 #> #> Slot "entrez_ids": #> # A tibble: 6 x 3 #> variant_id gene_name entrez_id #> <chr> <chr> <chr> #> 1 rs56261590 ANKRD17 26057 #> 2 rs56261590 HMGA1P2 171559 #> 3 rs56261590 LOC102724832 102724832 #> 4 rs4725504 DPP6 1804 #> 5 rs4725504 PAXBP1P1 106481704 #> 6 rs4725504 LOC107986750 107986750 #>
# Intersect common traits intersect(traits_ex01, traits_ex02)
#> An object of class "traits" #> Slot "traits": #> # A tibble: 1 x 3 #> efo_id trait uri #> <chr> <chr> <chr> #> 1 EFO_0004884 breast size http://www.ebi.ac.uk/efo/EFO_0004884 #>
# # setdiff() # # Remove studies from ex01 that are also present in ex02 setdiff(studies_ex01, studies_ex02)
#> An object of class "studies" #> Slot "studies": #> # A tibble: 1 x 13 #> study_id reported_trait initial_sample_… replication_sam… gxe gxg #> <chr> <chr> <chr> <chr> <lgl> <lgl> #> 1 GCST003… Breast size 33,790 European… <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: 1 x 2 #> study_id genotyping_technology #> <chr> <chr> #> 1 GCST003985 Genome-wide genotyping array #> #> Slot "platforms": #> # A tibble: 1 x 2 #> study_id manufacturer #> <chr> <chr> #> 1 GCST003985 Illumina #> #> Slot "ancestries": #> # A tibble: 1 x 4 #> study_id ancestry_id type number_of_individuals #> <chr> <int> <chr> <int> #> 1 GCST003985 1 initial 33790 #> #> Slot "ancestral_groups": #> # A tibble: 1 x 3 #> study_id ancestry_id ancestral_group #> <chr> <int> <chr> #> 1 GCST003985 1 European #> #> Slot "countries_of_origin": #> # A tibble: 1 x 5 #> study_id ancestry_id country_name major_area region #> <chr> <int> <chr> <chr> <chr> #> 1 GCST003985 1 <NA> <NA> <NA> #> #> Slot "countries_of_recruitment": #> # A tibble: 1 x 5 #> study_id ancestry_id country_name major_area region #> <chr> <int> <chr> <chr> <chr> #> 1 GCST003985 1 <NA> <NA> <NA> #> #> Slot "publications": #> # A tibble: 1 x 7 #> study_id pubmed_id publication_date publication title author_fullname #> <chr> <int> <date> <chr> <chr> <chr> #> 1 GCST003… 27182965 2016-05-15 Nat Genet Dete… Pickrell JK #> # … with 1 more variable: author_orcid <chr> #>
# Remove associations from ex01 that are also present in ex02 setdiff(associations_ex01, associations_ex02)
#> An object of class "associations" #> Slot "associations": #> # A tibble: 3 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 #> # … 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: 3 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 #> #> Slot "risk_alleles": #> # A tibble: 3 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 #> # … with 1 more variable: limited_list <lgl> #> #> Slot "genes": #> # A tibble: 7 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 #> #> Slot "ensembl_ids": #> # A tibble: 7 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 #> #> Slot "entrez_ids": #> # A tibble: 7 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 #>
# Remove variants from ex01 that are also present in ex02 setdiff(variants_ex01, variants_ex02)
#> An object of class "variants" #> Slot "variants": #> # A tibble: 1 x 7 #> variant_id merged functional_class chromosome_name chromosome_posi… #> <chr> <int> <chr> <chr> <int> #> 1 rs1469924… 0 regulatory_regi… 8 36984538 #> # … with 2 more variables: chromosome_region <chr>, last_update_date <dttm> #> #> Slot "genomic_contexts": #> # A tibble: 10 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 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: 4 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 #> #> Slot "entrez_ids": #> # A tibble: 6 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 #>
# Remove traits from ex01 that are also present in ex02 setdiff(traits_ex01, traits_ex02)
#> An object of class "traits" #> Slot "traits": #> # A tibble: 2 x 3 #> efo_id trait uri #> <chr> <chr> <chr> #> 1 EFO_0004343 waist-hip ratio http://www.ebi.ac.uk/efo/EFO_0004343 #> 2 EFO_0005299 non-word reading http://www.ebi.ac.uk/efo/EFO_0005299 #>
# # setequal() # # Compare two studies objects setequal(studies_ex01, studies_ex01)
#> [1] TRUE
setequal(studies_ex01, studies_ex02)
#> [1] FALSE
# Compare two associations objects setequal(associations_ex01, associations_ex01)
#> [1] TRUE
setequal(associations_ex01, associations_ex02)
#> [1] FALSE
# Compare two variants objects setequal(variants_ex01, variants_ex01)
#> [1] TRUE
setequal(variants_ex01, variants_ex02)
#> [1] FALSE
# Compare two traits objects setequal(traits_ex01, traits_ex01)
#> [1] TRUE
setequal(traits_ex01, traits_ex02)
#> [1] FALSE