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

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

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

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

Arguments

x

A variants 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 variants object.

Examples

# Subset a variants object by identifier variants_ex01['rs4725504']
#> 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 rs4725504 0 intergenic_vari… 7 153608338 #> # … with 2 more variables: chromosome_region <chr>, last_update_date <dttm> #> #> Slot "genomic_contexts": #> # A tibble: 4 x 11 #> variant_id gene_name chromosome_name chromosome_posi… distance is_closest_gene #> <chr> <chr> <chr> <int> <int> <lgl> #> 1 rs4725504 DPP6 7 153608338 278759 TRUE #> 2 rs4725504 DPP6 7 153608338 139795 TRUE #> 3 rs4725504 PAXBP1P1 7 153608338 158463 TRUE #> 4 rs4725504 LOC10798… 7 153608338 84107 TRUE #> # … with 5 more variables: is_intergenic <lgl>, is_upstream <lgl>, #> # is_downstream <lgl>, source <chr>, mapping_method <chr> #> #> Slot "ensembl_ids": #> # A tibble: 2 x 3 #> variant_id gene_name ensembl_id #> <chr> <chr> <chr> #> 1 rs4725504 DPP6 ENSG00000130226 #> 2 rs4725504 PAXBP1P1 ENSG00000233489 #> #> Slot "entrez_ids": #> # A tibble: 3 x 3 #> variant_id gene_name entrez_id #> <chr> <chr> <chr> #> 1 rs4725504 DPP6 1804 #> 2 rs4725504 PAXBP1P1 106481704 #> 3 rs4725504 LOC107986750 107986750 #>
# Or by its position in table variants variants_ex01[3]
#> 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 rs4725504 0 intergenic_vari… 7 153608338 #> # … with 2 more variables: chromosome_region <chr>, last_update_date <dttm> #> #> Slot "genomic_contexts": #> # A tibble: 4 x 11 #> variant_id gene_name chromosome_name chromosome_posi… distance is_closest_gene #> <chr> <chr> <chr> <int> <int> <lgl> #> 1 rs4725504 DPP6 7 153608338 278759 TRUE #> 2 rs4725504 DPP6 7 153608338 139795 TRUE #> 3 rs4725504 PAXBP1P1 7 153608338 158463 TRUE #> 4 rs4725504 LOC10798… 7 153608338 84107 TRUE #> # … with 5 more variables: is_intergenic <lgl>, is_upstream <lgl>, #> # is_downstream <lgl>, source <chr>, mapping_method <chr> #> #> Slot "ensembl_ids": #> # A tibble: 2 x 3 #> variant_id gene_name ensembl_id #> <chr> <chr> <chr> #> 1 rs4725504 DPP6 ENSG00000130226 #> 2 rs4725504 PAXBP1P1 ENSG00000233489 #> #> Slot "entrez_ids": #> # A tibble: 3 x 3 #> variant_id gene_name entrez_id #> <chr> <chr> <chr> #> 1 rs4725504 DPP6 1804 #> 2 rs4725504 PAXBP1P1 106481704 #> 3 rs4725504 LOC107986750 107986750 #>
# Keep all variants except the third variants_ex01[-3]
#> 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 rs1469924… 0 regulatory_regi… 8 36984538 #> 2 rs56261590 0 intron_variant 4 73189781 #> # … with 2 more variables: chromosome_region <chr>, last_update_date <dttm> #> #> Slot "genomic_contexts": #> # A tibble: 17 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 #> 11 rs56261590 ANKRD17 4 73189781 0 #> 12 rs56261590 ANKRD17 4 73189781 0 #> 13 rs56261590 HMGA1P2 4 73189781 90636 #> 14 rs56261590 HMGA1P2 4 73189781 89275 #> 15 rs56261590 LOC10272… 4 73189781 69394 #> 16 rs56261590 AC053527… 4 73189781 69428 #> 17 rs56261590 RF00334 4 73189781 74179 #> # … 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: 8 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 #> #> Slot "entrez_ids": #> # A tibble: 9 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 #>