You can subset associations by identifier or by position using the
`[` operator.
Usage
# 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 × 17
#> association_id pvalue pvalue_description pvalue_mantissa pvalue_exponent
#> <chr> <dbl> <chr> <int> <int>
#> 1 22505 0.000007 NA 7 -6
#> # 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 22505 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 22505 1 chr22:45895495 T NA NA
#> # ℹ 1 more variable: limited_list <lgl>
#>
#> Slot "genes":
#> # A tibble: 2 × 3
#> association_id locus_id gene_name
#> <chr> <int> <chr>
#> 1 22505 1 TBC1D22A
#> 2 22505 1 LOC100128818
#>
#> Slot "ensembl_ids":
#> # A tibble: 2 × 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 × 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 × 17
#> association_id pvalue pvalue_description pvalue_mantissa pvalue_exponent
#> <chr> <dbl> <chr> <int> <int>
#> 1 22505 0.000007 NA 7 -6
#> # 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 22505 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 22505 1 chr22:45895495 T NA NA
#> # ℹ 1 more variable: limited_list <lgl>
#>
#> Slot "genes":
#> # A tibble: 2 × 3
#> association_id locus_id gene_name
#> <chr> <int> <chr>
#> 1 22505 1 TBC1D22A
#> 2 22505 1 LOC100128818
#>
#> Slot "ensembl_ids":
#> # A tibble: 2 × 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 × 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 × 17
#> association_id pvalue pvalue_description pvalue_mantissa pvalue_exponent
#> <chr> <dbl> <chr> <int> <int>
#> 1 22509 3e- 9 NA 3 -9
#> 2 19537565 7e-31 NA 7 -31
#> 3 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: 3 × 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 × 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
#> # 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 19537565 1 KCNU1
#> 5 19537565 1 ZNF703
#> 6 19537593 1 CCDC170
#> 7 19537593 1 ESR1
#>
#> 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 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 × 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
#>