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.
Arguments
- x, y
Objects of either class studies, associations, variants, or traits.
- ...
other arguments passed on to methods.
Examples
#
# union()
#
# Combine studies and remove duplicates
union(studies_ex01, studies_ex02)
#> An object of class "studies"
#> Slot "studies":
#> # A tibble: 3 × 13
#> study_id reported_trait initial_sample_size replication_sample_s…¹ gxe gxg
#> <chr> <chr> <chr> <chr> <lgl> <lgl>
#> 1 GCST001… Breast size 16,175 European an… NA FALSE FALSE
#> 2 GCST003… Breast size 33,790 European an… NA FALSE FALSE
#> 3 GCST006… Breast size 5,609 Japanese anc… NA FALSE FALSE
#> # ℹ abbreviated name: ¹replication_sample_size
#> # ℹ 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 × 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 × 2
#> study_id manufacturer
#> <chr> <chr>
#> 1 GCST001585 Illumina
#> 2 GCST003985 Illumina
#> 3 GCST006655 Affymetrix
#>
#> Slot "ancestries":
#> # A tibble: 3 × 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 × 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 × 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 × 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 × 7
#> study_id pubmed_id publication_date publication title author_fullname
#> <chr> <int> <date> <chr> <chr> <chr>
#> 1 GCST001585 22747683 2012-06-29 BMC Med Genet Genetic v… Eriksson N
#> 2 GCST003985 27182965 2016-05-15 Nat Genet Detection… Pickrell JK
#> 3 GCST006655 29855537 2018-05-30 Sci Rep Japanese … Hirata T
#> # ℹ 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 × 17
#> association_id pvalue pvalue_description pvalue_mantissa pvalue_exponent
#> <chr> <dbl> <chr> <int> <int>
#> 1 22509 3e- 9 NA 3 -9
#> 2 22505 7e- 6 NA 7 -6
#> 3 19537565 7e-31 NA 7 -31
#> 4 19537593 1e-11 NA 1 -11
#> 5 31665940 8e- 6 NA 8 -6
#> 6 34944736 6e- 9 NA 6 -9
#> # ℹ 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 × 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 × 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 chr22:45895495 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 rs146992477 TTCTTTCTTTC 0.381 FALSE
#> # ℹ 1 more variable: limited_list <lgl>
#>
#> Slot "genes":
#> # A tibble: 11 × 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 × 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 × 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 × 7
#> variant_id merged functional_class chromosome_name chromosome_position
#> <chr> <int> <chr> <chr> <int>
#> 1 rs146992477 0 regulatory_region_vari… 8 36984538
#> 2 rs56261590 0 intron_variant 4 73189781
#> 3 rs4725504 0 intergenic_variant 7 153608338
#> 4 rs11099757 0 intron_variant 4 150143216
#> 5 rs16871509 0 intergenic_variant 5 71726395
#> # ℹ 2 more variables: chromosome_region <chr>, last_update_date <dttm>
#>
#> Slot "genomic_contexts":
#> # A tibble: 33 × 11
#> variant_id gene_name chromosome_name chromosome_position distance
#> <chr> <chr> <chr> <int> <int>
#> 1 rs146992477 LOC105379377 8 36984538 81555
#> 2 rs146992477 KCNU1 8 36984538 48413
#> 3 rs146992477 LOC105379376 8 36984538 2533
#> 4 rs146992477 TPT1P8 8 36984538 95231
#> 5 rs146992477 RPL26P25 8 36984538 3392
#> 6 rs146992477 KCNU1 8 36984538 48413
#> 7 rs146992477 AC090453.1 8 36984538 3439
#> 8 rs146992477 TPT1P8 8 36984538 95008
#> 9 rs146992477 AC092818.1 8 36984538 82903
#> 10 rs146992477 LOC105379375 8 36984538 59331
#> # ℹ 23 more rows
#> # ℹ 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 × 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 × 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 × 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 × 13
#> study_id reported_trait initial_sample_size replication_sample_s…¹ gxe gxg
#> <chr> <chr> <chr> <chr> <lgl> <lgl>
#> 1 GCST001… Breast size 16,175 European an… NA FALSE FALSE
#> # ℹ abbreviated name: ¹replication_sample_size
#> # ℹ 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 × 2
#> study_id genotyping_technology
#> <chr> <chr>
#> 1 GCST001585 Genome-wide genotyping array
#>
#> Slot "platforms":
#> # A tibble: 1 × 2
#> study_id manufacturer
#> <chr> <chr>
#> 1 GCST001585 Illumina
#>
#> Slot "ancestries":
#> # A tibble: 1 × 4
#> study_id ancestry_id type number_of_individuals
#> <chr> <int> <chr> <int>
#> 1 GCST001585 1 initial 16175
#>
#> Slot "ancestral_groups":
#> # A tibble: 1 × 3
#> study_id ancestry_id ancestral_group
#> <chr> <int> <chr>
#> 1 GCST001585 1 European
#>
#> Slot "countries_of_origin":
#> # A tibble: 1 × 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 × 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 × 7
#> study_id pubmed_id publication_date publication title author_fullname
#> <chr> <int> <date> <chr> <chr> <chr>
#> 1 GCST001585 22747683 2012-06-29 BMC Med Genet Genetic v… Eriksson N
#> # ℹ 1 more variable: author_orcid <chr>
#>
# Intersect common associations
intersect(associations_ex01, associations_ex02)
#> An object of class "associations"
#> Slot "associations":
#> # A tibble: 1 × 17
#> association_id pvalue pvalue_description pvalue_mantissa pvalue_exponent
#> <chr> <dbl> <chr> <int> <int>
#> 1 19537593 1e-11 NA 1 -11
#> # ℹ 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 × 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 × 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
#> # ℹ 1 more variable: limited_list <lgl>
#>
#> Slot "genes":
#> # A tibble: 2 × 3
#> association_id locus_id gene_name
#> <chr> <int> <chr>
#> 1 19537593 1 CCDC170
#> 2 19537593 1 ESR1
#>
#> Slot "ensembl_ids":
#> # A tibble: 2 × 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 × 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 × 7
#> variant_id merged functional_class chromosome_name chromosome_position
#> <chr> <int> <chr> <chr> <int>
#> 1 rs56261590 0 intron_variant 4 73189781
#> 2 rs4725504 0 intergenic_variant 7 153608338
#> # ℹ 2 more variables: chromosome_region <chr>, last_update_date <dttm>
#>
#> Slot "genomic_contexts":
#> # A tibble: 11 × 11
#> variant_id gene_name chromosome_name chromosome_position 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 LOC102724832 4 73189781 69394
#> 6 rs56261590 AC053527.1 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 LOC107986750 7 153608338 84107
#> # ℹ 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 × 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 × 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 × 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 × 13
#> study_id reported_trait initial_sample_size replication_sample_s…¹ gxe gxg
#> <chr> <chr> <chr> <chr> <lgl> <lgl>
#> 1 GCST003… Breast size 33,790 European an… NA FALSE FALSE
#> # ℹ abbreviated name: ¹replication_sample_size
#> # ℹ 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 × 2
#> study_id genotyping_technology
#> <chr> <chr>
#> 1 GCST003985 Genome-wide genotyping array
#>
#> Slot "platforms":
#> # A tibble: 1 × 2
#> study_id manufacturer
#> <chr> <chr>
#> 1 GCST003985 Illumina
#>
#> Slot "ancestries":
#> # A tibble: 1 × 4
#> study_id ancestry_id type number_of_individuals
#> <chr> <int> <chr> <int>
#> 1 GCST003985 1 initial 33790
#>
#> Slot "ancestral_groups":
#> # A tibble: 1 × 3
#> study_id ancestry_id ancestral_group
#> <chr> <int> <chr>
#> 1 GCST003985 1 European
#>
#> Slot "countries_of_origin":
#> # A tibble: 1 × 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 × 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 × 7
#> study_id pubmed_id publication_date publication title author_fullname
#> <chr> <int> <date> <chr> <chr> <chr>
#> 1 GCST003985 27182965 2016-05-15 Nat Genet Detection a… Pickrell JK
#> # ℹ 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 × 17
#> association_id pvalue pvalue_description pvalue_mantissa pvalue_exponent
#> <chr> <dbl> <chr> <int> <int>
#> 1 22509 3e- 9 NA 3 -9
#> 2 22505 7e- 6 NA 7 -6
#> 3 19537565 7e-31 NA 7 -31
#> # ℹ 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 × 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 × 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 chr22:45895495 T NA NA
#> 3 19537565 1 rs10110651 NA NA FALSE
#> # ℹ 1 more variable: limited_list <lgl>
#>
#> Slot "genes":
#> # A tibble: 7 × 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 × 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 × 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 × 7
#> variant_id merged functional_class chromosome_name chromosome_position
#> <chr> <int> <chr> <chr> <int>
#> 1 rs146992477 0 regulatory_region_vari… 8 36984538
#> # ℹ 2 more variables: chromosome_region <chr>, last_update_date <dttm>
#>
#> Slot "genomic_contexts":
#> # A tibble: 10 × 11
#> variant_id gene_name chromosome_name chromosome_position distance
#> <chr> <chr> <chr> <int> <int>
#> 1 rs146992477 LOC105379377 8 36984538 81555
#> 2 rs146992477 KCNU1 8 36984538 48413
#> 3 rs146992477 LOC105379376 8 36984538 2533
#> 4 rs146992477 TPT1P8 8 36984538 95231
#> 5 rs146992477 RPL26P25 8 36984538 3392
#> 6 rs146992477 KCNU1 8 36984538 48413
#> 7 rs146992477 AC090453.1 8 36984538 3439
#> 8 rs146992477 TPT1P8 8 36984538 95008
#> 9 rs146992477 AC092818.1 8 36984538 82903
#> 10 rs146992477 LOC105379375 8 36984538 59331
#> # ℹ 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 × 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 × 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 × 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