This page documents functions using the IGVF REST API, documented at https://api.catalogkg.igvf.org/#.
Note that functions will only return a limited number
of responses, see limit and page arguments below for control
over number of responses.
gene_variants() locates variants associated with a gene.
Only one of gene_id, hgnc, gene_name, or alias
should be specified.
variant_genes() locates genes
associated with a variant.
Only one of spdi, hgvs, rsid, variant_id,
or chr + position should be specified.
gene_elements() locates elements
associated with a gene.
elements() locates genomic elements
based on a genomic range query.
element_genes() locates genomic elements and associated genes
based on a genomic range query.
Usage
gene_variants(
gene_id = NULL,
hgnc = NULL,
gene_name = NULL,
alias = NULL,
organism = "Homo sapiens",
log10pvalue = NULL,
effect_size = NULL,
page = 0L,
limit = 25L,
verbose = FALSE
)
variant_genes(
spdi = NULL,
hgvs = NULL,
rsid = NULL,
variant_id = NULL,
chr = NULL,
position = NULL,
organism = "Homo sapiens",
log10pvalue = NULL,
effect_size = NULL,
page = 0L,
limit = 25L,
verbose = FALSE
)
gene_elements(gene_id = NULL, page = 0L, limit = 25L, verbose = FALSE)
elements(range = NULL, page = 0L, limit = 25L)
element_genes(range = NULL, page = 0L, limit = 25L, verbose = FALSE)Arguments
- gene_id
character(1) Ensembl gene identifier, e.g., "ENSG00000106633"
- hgnc
character(1) HGNC identifier
- gene_name
character(1) Gene symbol, e.g., "GCK"
- alias
character(1) Gene alias
- organism
character(1) Either 'Homo sapiens' (default) or 'Mus musculus'
- log10pvalue
character(1) The following can be used to set thresholds on the negative log10pvalue: gt (>), gte (>=), lt (<), lte (<=), with a ":" following and a value, e.g., "gt:5.0"
- effect_size
character(1) Optional string used for thresholding on the effect size of the variant on the gene. See 'log10pvalue'. E.g., "gt:0.5"
- page
integer(1) when there are more response items than
limit, offers pagination. starts on page 0L, next is 1L, ...- limit
integer(1) the limit parameter controls the page size and can not exceed 1000
- verbose
logical(1) return additional information about variants and genes
- spdi
character(1) SPDI of variant
- hgvs
character(1) HGVS of variant
- rsid
character(1) RSID of variant
- variant_id
character(1) IGVF variant ID
- chr
character(1) UCSC-style chromosome name of variant, e.g. "chr1"
- position
character(1) 0-based position of variant
- range
the query GRanges (expects 1-based start position)
Value
gene_variants() returns a tibble describing variants
associated with the gene; use verbose = TRUE to retrieve more
extensive information.
variant_genes() returns a tibble describing genes
associated with a variant; use verbose = TRUE to retrieve more
extensive information.
gene_elements() returns a tibble describing elements
associated with the gene; use verbose = TRUE to retrieve more
extensive information.
elements() returns a GRanges object describing elements.
element_genes() returns a tibble describing genomic element and gene pairs.
Examples
rigvf::gene_variants(gene_name = "GCK")
#> # A tibble: 25 × 19
#> gene sequence_variant effect_size neg_log10_pvalue posterior_inclusion_…¹
#> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 genes/E… variants/NC_000… -1.01 9.06 0.0599
#> 2 genes/E… variants/NC_000… -0.347 7.93 0.200
#> 3 genes/E… variants/NC_000… -0.565 6.93 0.103
#> 4 genes/E… variants/NC_000… 0.378 8.22 0.0720
#> 5 genes/E… variants/NC_000… -0.319 6.92 0.0422
#> 6 genes/E… variants/NC_000… 0.349 7.54 0.0170
#> 7 genes/E… variants/NC_000… -1.02 9.39 0.144
#> 8 genes/E… variants/NC_000… -0.340 10.2 0.0234
#> 9 genes/E… variants/NC_000… -0.486 7.03 0.0129
#> 10 genes/E… variants/NC_000… 0.262 4.45 0.138
#> # ℹ 15 more rows
#> # ℹ abbreviated name: ¹posterior_inclusion_probability
#> # ℹ 14 more variables: standard_error <dbl>, z_score <dbl>,
#> # credible_set_min_r2 <dbl>, method <chr>, source <chr>, source_url <chr>,
#> # label <chr>, p_value <dbl>, biological_context <chr>, biosample_term <chr>,
#> # study <chr>, name <chr>, class <chr>, files_filesets <chr>
rigvf::gene_variants(gene_name = "GCK", effect_size="gt:0.5")
#> # A tibble: 0 × 0
rigvf::gene_variants(gene_name = "GCK", verbose = TRUE)
#> # A tibble: 25 × 19
#> gene sequence_variant effect_size neg_log10_pvalue
#> <list> <list> <dbl> <dbl>
#> 1 <named list [15]> <named list [15]> -1.01 9.06
#> 2 <named list [15]> <named list [15]> -0.347 7.93
#> 3 <named list [15]> <named list [15]> -0.565 6.93
#> 4 <named list [15]> <named list [15]> 0.378 8.22
#> 5 <named list [15]> <named list [15]> -0.319 6.92
#> 6 <named list [15]> <named list [15]> 0.349 7.54
#> 7 <named list [15]> <named list [15]> -1.02 9.39
#> 8 <named list [15]> <named list [15]> -0.340 10.2
#> 9 <named list [15]> <named list [15]> -0.486 7.03
#> 10 <named list [15]> <named list [15]> 0.262 4.45
#> # ℹ 15 more rows
#> # ℹ 15 more variables: posterior_inclusion_probability <dbl>,
#> # standard_error <dbl>, z_score <dbl>, credible_set_min_r2 <dbl>,
#> # method <chr>, source <chr>, source_url <chr>, label <chr>, p_value <dbl>,
#> # biological_context <chr>, biosample_term <chr>, study <list>, name <chr>,
#> # class <chr>, files_filesets <chr>
rigvf::variant_genes(spdi = "NC_000001.11:920568:G:A")
#> # A tibble: 0 × 0
rigvf::gene_elements(gene_id = "ENSG00000187961")
#> # A tibble: 25 × 27
#> name label method class source source_url biological_context biosample_term
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 2 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 3 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 4 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 5 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 6 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 7 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 8 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 9 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> 10 expre… regu… Pertu… obse… IGVF https://d… HCASMC-hTERT ontology_term…
#> # ℹ 15 more rows
#> # ℹ 19 more variables: cell_annotation <list>, cell_annotation_term <list>,
#> # files_filesets <chr>, crispr_modality <chr>, score <list>,
#> # transcription_start_site <list>, rna_pseudobulk_tpm <list>, log2FC <dbl>,
#> # effect_size <list>, z_score <list>, t_score <list>, idr <list>,
#> # p_value <dbl>, p_value_adj <dbl>, neg_log10_pvalue <dbl>,
#> # neg_log10_pvalue_adj <dbl>, significant <lgl>, genomic_element <chr>, …
rng <- GenomicRanges::GRanges("chr1", IRanges::IRanges(1157520,1158189))
rigvf::elements(range = rng)
#> GRanges object with 25 ranges and 5 metadata columns:
#> seqnames ranges strand | name
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 1157437-1157782 * | EH38E2777055
#> [2] chr1 1157886-1158053 * | EH38E2777056
#> [3] chr1 1158136-1158445 * | EH38E1310547
#> [4] chr1 1156965-1157764 * | enhancer_chr1_115696..
#> [5] chr1 1156972-1157746 * | enhancer_chr1_115697..
#> ... ... ... ... . ...
#> [21] chr1 1156585-1157825 * | intergenic_chr1_1156..
#> [22] chr1 1156586-1158733 * | intergenic_chr1_1156..
#> [23] chr1 1156595-1157836 * | intergenic_chr1_1156..
#> [24] chr1 1156595-1158733 * | intergenic_chr1_1156..
#> [25] chr1 1156609-1158905 * | intergenic_chr1_1156..
#> source_annotation type source
#> <character> <character> <character>
#> [1] dELS: distal Enhance.. candidate cis regula.. ENCODE
#> [2] dELS: distal Enhance.. candidate cis regula.. ENCODE
#> [3] dELS: distal Enhance.. candidate cis regula.. ENCODE
#> [4] enhancer accessible dna eleme.. IGVF
#> [5] enhancer accessible dna eleme.. IGVF
#> ... ... ... ...
#> [21] intergenic accessible dna eleme.. ENCODE
#> [22] intergenic accessible dna eleme.. ENCODE
#> [23] intergenic accessible dna eleme.. ENCODE
#> [24] intergenic accessible dna eleme.. ENCODE
#> [25] intergenic accessible dna eleme.. ENCODE
#> source_url
#> <character>
#> [1] https://www.encodepr..
#> [2] https://www.encodepr..
#> [3] https://www.encodepr..
#> [4] https://data.igvf.or..
#> [5] https://data.igvf.or..
#> ... ...
#> [21] https://www.encodepr..
#> [22] https://www.encodepr..
#> [23] https://www.encodepr..
#> [24] https://www.encodepr..
#> [25] https://www.encodepr..
#> -------
#> seqinfo: 1 sequence from hg38 genome; no seqlengths
rigvf::element_genes(range = rng)
#> # A tibble: 25 × 27
#> name label method class source source_url biological_context biosample_term
#> <chr> <chr> <chr> <chr> <chr> <chr> <list> <list>
#> 1 regul… pred… scE2G pred… IGVF https://d… <chr [1]> <chr [1]>
#> 2 regul… pred… scE2G pred… IGVF https://d… <chr [1]> <chr [1]>
#> 3 regul… pred… scE2G pred… IGVF https://d… <NULL> <NULL>
#> 4 regul… pred… ENCOD… pred… ENCODE https://w… <chr [1]> <chr [1]>
#> 5 regul… pred… ENCOD… pred… ENCODE https://w… <chr [1]> <chr [1]>
#> 6 regul… pred… ENCOD… pred… ENCODE https://w… <chr [1]> <chr [1]>
#> 7 regul… pred… ENCOD… pred… ENCODE https://w… <chr [1]> <chr [1]>
#> 8 regul… pred… ENCOD… pred… ENCODE https://w… <chr [1]> <chr [1]>
#> 9 regul… pred… ENCOD… pred… ENCODE https://w… <chr [1]> <chr [1]>
#> 10 regul… pred… ENCOD… pred… ENCODE https://w… <chr [1]> <chr [1]>
#> # ℹ 15 more rows
#> # ℹ 19 more variables: cell_annotation <list>, cell_annotation_term <list>,
#> # files_filesets <chr>, crispr_modality <list>, score <dbl>,
#> # transcription_start_site <list>, rna_pseudobulk_tpm <list>, log2FC <list>,
#> # effect_size <list>, z_score <list>, t_score <list>, idr <list>,
#> # p_value <list>, p_value_adj <list>, neg_log10_pvalue <list>,
#> # neg_log10_pvalue_adj <list>, significant <list>, genomic_element <chr>, …