You can subset associations by identifier or by position using the `[` operator.

# S4 method for associations,missing,missing,missing
[(x, i, j, ...,
  drop = FALSE)

# S4 method for associations,numeric,missing,missing
[(x, i, j, ...,
  drop = FALSE)

# S4 method for associations,character,missing,missing
[(x, i, j, ...,
  drop = FALSE)

Arguments

x

A associations object.

i

Position of the identifier or the name of the identifier itself.

j

Not used.

...

Additional arguments not used here.

drop

Not used.

Value

A associations object.

Examples

# Subset an associations object by identifier associations_ex01['22505']
#> 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 22505 7.00e-6 NA 7 -6 #> # … 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 22505 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 22505 1 chr22:458… T NA NA #> # … with 1 more variable: limited_list <lgl> #> #> Slot "genes": #> # A tibble: 2 x 3 #> association_id locus_id gene_name #> <chr> <int> <chr> #> 1 22505 1 TBC1D22A #> 2 22505 1 LOC100128818 #> #> Slot "ensembl_ids": #> # A tibble: 2 x 4 #> association_id locus_id gene_name ensembl_id #> <chr> <int> <chr> <chr> #> 1 22505 1 TBC1D22A ENSG00000054611 #> 2 22505 1 LOC100128818 NA #> #> Slot "entrez_ids": #> # A tibble: 2 x 4 #> association_id locus_id gene_name entrez_id #> <chr> <int> <chr> <chr> #> 1 22505 1 TBC1D22A 25771 #> 2 22505 1 LOC100128818 NA #>
# Or by its position in table associations associations_ex01[2]
#> 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 22505 7.00e-6 NA 7 -6 #> # … 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 22505 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 22505 1 chr22:458… T NA NA #> # … with 1 more variable: limited_list <lgl> #> #> Slot "genes": #> # A tibble: 2 x 3 #> association_id locus_id gene_name #> <chr> <int> <chr> #> 1 22505 1 TBC1D22A #> 2 22505 1 LOC100128818 #> #> Slot "ensembl_ids": #> # A tibble: 2 x 4 #> association_id locus_id gene_name ensembl_id #> <chr> <int> <chr> <chr> #> 1 22505 1 TBC1D22A ENSG00000054611 #> 2 22505 1 LOC100128818 NA #> #> Slot "entrez_ids": #> # A tibble: 2 x 4 #> association_id locus_id gene_name entrez_id #> <chr> <int> <chr> <chr> #> 1 22505 1 TBC1D22A 25771 #> 2 22505 1 LOC100128818 NA #>
# Keep all associations except the second associations_ex01[-2]
#> 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 19537565 7.00e-31 NA 7 -31 #> 3 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: 3 x 4 #> association_id locus_id haplotype_snp_count description #> <chr> <int> <int> <chr> #> 1 22509 1 NA Single variant #> 2 19537565 1 NA Single variant #> 3 19537593 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 19537565 1 rs10110651 NA NA FALSE #> 3 19537593 1 rs9397437 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 19537565 1 KCNU1 #> 5 19537565 1 ZNF703 #> 6 19537593 1 CCDC170 #> 7 19537593 1 ESR1 #> #> 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 19537565 1 KCNU1 ENSG00000215262 #> 5 19537565 1 ZNF703 ENSG00000183779 #> 6 19537593 1 CCDC170 ENSG00000120262 #> 7 19537593 1 ESR1 ENSG00000091831 #> #> 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 19537565 1 KCNU1 157855 #> 5 19537565 1 ZNF703 80139 #> 6 19537593 1 CCDC170 80129 #> 7 19537593 1 ESR1 2099 #>