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Get Neighbor Gene

Source: R/get_neighbor_gene.R
get_neighbor_gene.Rd

Find all neighboring genes on a certain chromosome around a position with a certain window size.

GTEx API Portal documentation

Usage

get_neighbor_gene(
  pos,
  chromosome,
  bp_window,
  page = 0,
  gencodeVersion = "v26",
  genomeBuild = "GRCh38/hg38",
  itemsPerPage = getOption("gtexr.itemsPerPage"),
  .verbose = getOption("gtexr.verbose"),
  .return_raw = FALSE
)

Arguments

pos

Integer.

chromosome

String. One of "chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrM", "chrX", "chrY".

bp_window

Integer.

page

Integer (default = 0).

gencodeVersion

String (default = "v26"). GENCODE annotation release. Either "v26" or "v19".

genomeBuild

String. Options: "GRCh38/hg38", "GRCh37/hg19". Default = "GRCh38/hg38".

itemsPerPage

Integer (default = 250). Set globally to maximum value 100000 with options(list(gtexr.itemsPerPage = 100000)).

.verbose

Logical. If TRUE (default), print paging information. Set to FALSE globally with options(list(gtexr.verbose = FALSE)).

.return_raw

Logical. If TRUE, return the raw API JSON response. Default = FALSE

Value

A tibble. Or a list if .return_raw = TRUE.

See also

Other Reference Genome Endpoints: get_exons(), get_gene_search(), get_genes(), get_genomic_features(), get_gwas_catalog_by_location(), get_transcripts()

Examples

get_neighbor_gene(pos = 1000000, chromosome = "chr1", bp_window = 10000)
#> 
#> ── Paging info ─────────────────────────────────────────────────────────────────
#> • numberOfPages = 1
#> • page = 0
#> • maxItemsPerPage = 250
#> • totalNumberOfItems = 4
#> # A tibble: 4 × 15
#>   chromosome dataSource description      end gencodeId gencodeVersion geneStatus
#>   <chr>      <chr>      <chr>          <int> <chr>     <chr>          <chr>     
#> 1 chr1       HAVANA     novel transc… 9.98e5 ENSG0000… v26            ""        
#> 2 chr1       HAVANA     hes family b… 1.00e6 ENSG0000… v26            ""        
#> 3 chr1       HAVANA     ISG15 ubiqui… 1.01e6 ENSG0000… v26            ""        
#> 4 chr1       HAVANA     ribosomal pr… 1.01e6 ENSG0000… v26            ""        
#> # ℹ 8 more variables: geneSymbol <chr>, geneSymbolUpper <chr>, geneType <chr>,
#> #   genomeBuild <chr>, start <int>, strand <chr>, tss <int>, entrezGeneId <int>