edges() and nodes() identify edges or nodes in the
data base.
db_gene_variants() locates variants associated with a
(Ensembl) gene identifier.
db_gene_elements() locates genomic elements associated with a
(Ensembl) gene identifier.
Usage
db_edges(
username = rigvf_config$get("username"),
password = rigvf_config$get("password")
)
db_nodes(
username = rigvf_config$get("username"),
password = rigvf_config$get("password")
)
db_gene_variants(
gene_id,
threshold,
username = rigvf_config$get("username"),
password = rigvf_config$get("password")
)
db_gene_elements(
gene_id,
threshold,
username = rigvf_config$get("username"),
password = rigvf_config$get("password")
)Arguments
- username
character(1) ArangoDB user name. Default: "guest".
- password
character(1) ArangoDB password. Default: "guestigvfcatalog". A better practice is to use an environment variable to record the password, rather than encoding in a script, so
password = Sys.getenv("RIGVF_ARANGODB_PASSWORD").- gene_id
character(1) Ensembl gene identifier
- threshold
numeric(1) minimum association statistic, minus log10 p-value for variants, and score for elements
Value
edges() and nodes() return a tibble with the edge or
node name and count of occurrences in the database.
db_gene_variants() returns a tibble summarizing variants
associated with the gene.
db_gene_elements() returns a tibble summarizing genomic elements
associated with the gene.
Examples
db_edges()
#> # A tibble: 34 × 2
#> name count
#> <chr> <dbl>
#> 1 variants_variants 5362104968
#> 2 variants_coding_variants 239116929
#> 3 coding_variants_proteins 238602987
#> 4 variants_genes_terms 95728528
#> 5 variants_genes 95728517
#> 6 genomic_elements_genes 31514158
#> 7 transcripts_genes_structure 4835125
#> 8 genes_genes 3553547
#> 9 variants_proteins 2927999
#> 10 mm_transcripts_mm_genes_structure 2417458
#> # ℹ 24 more rows
db_nodes()
#> # A tibble: 19 × 2
#> name count
#> <chr> <dbl>
#> 1 variants 1185310425
#> 2 coding_variants 239116929
#> 3 mm_variants 101894574
#> 4 genomic_elements 17833721
#> 5 genes_structure 4835125
#> 6 mm_genes_structure 2417758
#> 7 mm_genomic_elements 926826
#> 8 ontology_terms 731807
#> 9 proteins 290309
#> 10 transcripts 274031
#> 11 mm_transcripts 149547
#> 12 genes 69222
#> 13 mm_genes 56941
#> 14 studies 22690
#> 15 drugs 4613
#> 16 pathways 2711
#> 17 complexes 1681
#> 18 motifs 401
#> 19 donors 231
db_gene_variants("ENSG00000106633", threshold = 4.0)
#> # A tibble: 1,000 × 14
#> `_key` `_id` `_from` `_to` `_rev` biological_context chr p_value
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
#> 1 a6cbc153279e78b… vari… varian… gene… _i42_… esophagus muscula… chr7 5.82e-12
#> 2 fe37460fd352499… vari… varian… gene… _i42_… esophagus muscula… chr7 3.55e- 5
#> 3 541cb07e388227c… vari… varian… gene… _i42_… esophagus muscula… chr7 9.43e-12
#> 4 f926f23ed97a1ae… vari… varian… gene… _i42_… esophagus muscula… chr7 9.43e-12
#> 5 4600cd627888076… vari… varian… gene… _i42_… esophagus muscula… chr7 4.17e-12
#> 6 0642a7286da19b2… vari… varian… gene… _i42_… esophagus muscula… chr7 3.58e- 5
#> 7 b2b44a8a0e56c9b… vari… varian… gene… _i42_… esophagus muscula… chr7 2.94e- 5
#> 8 3808659e1f51104… vari… varian… gene… _i42_… esophagus muscula… chr7 2.68e- 5
#> 9 838b2fe5120da15… vari… varian… gene… _i42_… esophagus muscula… chr7 2.03e- 5
#> 10 a6cd41ca17f99aa… vari… varian… gene… _i42_… esophagus muscula… chr7 1.09e-12
#> # ℹ 990 more rows
#> # ℹ 6 more variables: log10pvalue <dbl>, effect_size <dbl>, pval_beta <dbl>,
#> # label <chr>, source <chr>, source_url <chr>
db_gene_elements("ENSG00000106633", threshold = 0.5)
#> # A tibble: 103 × 12
#> `_key` `_id` `_from` `_to` `_rev` score source source_url file_accession
#> <chr> <chr> <chr> <chr> <chr> <dbl> <chr> <chr> <chr>
#> 1 genic_chr7… geno… genomi… gene… _jI7z… 0.524 ENCOD… https://w… ENCFF009QHG
#> 2 genic_chr7… geno… genomi… gene… _jI7z… 0.961 ENCOD… https://w… ENCFF009QHG
#> 3 genic_chr7… geno… genomi… gene… _jI7z… 0.621 ENCOD… https://w… ENCFF009QHG
#> 4 promoter_c… geno… genomi… gene… _jI7z… 0.974 ENCOD… https://w… ENCFF009QHG
#> 5 genic_chr7… geno… genomi… gene… _jI70… 0.989 ENCOD… https://w… ENCFF057RTZ
#> 6 promoter_c… geno… genomi… gene… _jI70… 0.869 ENCOD… https://w… ENCFF057RTZ
#> 7 genic_chr7… geno… genomi… gene… _jI71… 0.942 ENCOD… https://w… ENCFF059DHV
#> 8 genic_chr7… geno… genomi… gene… _jI71… 0.574 ENCOD… https://w… ENCFF059DHV
#> 9 genic_chr7… geno… genomi… gene… _jI71… 0.828 ENCOD… https://w… ENCFF059DHV
#> 10 promoter_c… geno… genomi… gene… _jI71… 0.929 ENCOD… https://w… ENCFF059DHV
#> # ℹ 93 more rows
#> # ℹ 3 more variables: biological_context <chr>, name <chr>, inverse_name <chr>