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 × 12
#> sequence_variant gene study label log10pvalue effect_size method source
#> <chr> <chr> <chr> <chr> <dbl> <list> <list> <chr>
#> 1 variants/NC_000007.1… gene… stud… spli… 9.06 <NULL> <NULL> EBI e…
#> 2 variants/NC_000007.1… gene… stud… eQTL 7.93 <NULL> <NULL> EBI e…
#> 3 variants/NC_000007.1… gene… stud… eQTL 6.93 <NULL> <NULL> EBI e…
#> 4 variants/NC_000007.1… gene… stud… eQTL 8.22 <NULL> <NULL> EBI e…
#> 5 variants/NC_000007.1… gene… stud… eQTL 6.92 <NULL> <NULL> EBI e…
#> 6 variants/NC_000007.1… gene… stud… eQTL 7.54 <NULL> <NULL> EBI e…
#> 7 variants/NC_000007.1… gene… stud… spli… 9.39 <NULL> <NULL> EBI e…
#> 8 variants/NC_000007.1… gene… stud… eQTL 10.2 <NULL> <NULL> EBI e…
#> 9 variants/NC_000007.1… gene… stud… eQTL 7.03 <NULL> <NULL> EBI e…
#> 10 variants/NC_000007.1… gene… stud… eQTL 4.45 <NULL> <NULL> EBI e…
#> # ℹ 15 more rows
#> # ℹ 4 more variables: source_url <chr>, biological_context <chr>, chr <list>,
#> # name <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 × 12
#> sequence_variant gene study label log10pvalue effect_size
#> <list> <list> <list> <chr> <dbl> <list>
#> 1 <named list [16]> <named list> <named list> splice_Q… 9.06 <NULL>
#> 2 <named list [16]> <named list> <named list> eQTL 7.93 <NULL>
#> 3 <named list [16]> <named list> <named list> eQTL 6.93 <NULL>
#> 4 <named list [16]> <named list> <named list> eQTL 8.22 <NULL>
#> 5 <named list [16]> <named list> <named list> eQTL 6.92 <NULL>
#> 6 <named list [16]> <named list> <named list> eQTL 7.54 <NULL>
#> 7 <named list [16]> <named list> <named list> splice_Q… 9.39 <NULL>
#> 8 <named list [16]> <named list> <named list> eQTL 10.2 <NULL>
#> 9 <named list [16]> <named list> <named list> eQTL 7.03 <NULL>
#> 10 <named list [16]> <named list> <named list> eQTL 4.45 <NULL>
#> # ℹ 15 more rows
#> # ℹ 6 more variables: method <list>, source <chr>, source_url <chr>,
#> # biological_context <chr>, chr <list>, name <chr>
rigvf::variant_genes(spdi = "NC_000001.11:920568:G:A")
#> # A tibble: 0 × 0
res <- rigvf::gene_elements(gene_id = "ENSG00000187961")
res
#> # A tibble: 1 × 2
#> gene elements
#> <list> <list>
#> 1 <named list [5]> <list [25]>
res |>
tidyr::unnest_longer(elements) |>
tidyr::unnest_wider(elements)
#> # A tibble: 25 × 14
#> gene id cell_type score model dataset element_type element_chr
#> <list> <chr> <chr> <lgl> <chr> <chr> <chr> <chr>
#> 1 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr1
#> 2 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr1
#> 3 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr1
#> 4 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr1
#> 5 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr1
#> 6 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr1
#> 7 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr1
#> 8 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr1
#> 9 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr10
#> 10 <named list [5]> geno… CD8-posi… NA IGVF https:… tested elem… chr10
#> # ℹ 15 more rows
#> # ℹ 6 more variables: element_start <int>, element_end <int>, name <chr>,
#> # method <chr>, class <chr>, files_filesets <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 1156360-1158596 * | intergenic_chr1_1156..
#> [5] chr1 1156375-1158325 * | intergenic_chr1_1156..
#> ... ... ... ... . ...
#> [21] chr1 1156595-1158733 * | intergenic_chr1_1156..
#> [22] chr1 1156609-1158905 * | intergenic_chr1_1156..
#> [23] chr1 1156629-1157810 * | intergenic_chr1_1156..
#> [24] chr1 1156631-1157834 * | intergenic_chr1_1156..
#> [25] chr1 1156638-1159033 * | 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] intergenic accessible dna eleme.. ENCODE
#> [5] intergenic accessible dna eleme.. ENCODE
#> ... ... ... ...
#> [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://www.encodepr..
#> [5] https://www.encodepr..
#> ... ...
#> [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 × 11
#> score source source_url significant genomic_element gene biosample name
#> <dbl> <chr> <chr> <list> <chr> <chr> <chr> <chr>
#> 1 0.335 ENCODE https://www.e… <NULL> genomic_elemen… gene… stomach … regu…
#> 2 0.431 ENCODE https://www.e… <NULL> genomic_elemen… gene… stomach … regu…
#> 3 0.971 ENCODE https://www.e… <NULL> genomic_elemen… gene… stomach … regu…
#> 4 0.501 ENCODE https://www.e… <NULL> genomic_elemen… gene… stomach … regu…
#> 5 0.869 ENCODE https://www.e… <NULL> genomic_elemen… gene… stomach … regu…
#> 6 0.886 ENCODE https://www.e… <NULL> genomic_elemen… gene… stomach … regu…
#> 7 0.773 ENCODE https://www.e… <NULL> genomic_elemen… gene… stomach … regu…
#> 8 0.372 ENCODE https://www.e… <NULL> genomic_elemen… gene… ovary fr… regu…
#> 9 0.730 ENCODE https://www.e… <NULL> genomic_elemen… gene… T-helper… regu…
#> 10 0.564 ENCODE https://www.e… <NULL> genomic_elemen… gene… T-helper… regu…
#> # ℹ 15 more rows
#> # ℹ 3 more variables: method <chr>, class <chr>, files_filesets <chr>