get_neighbor_gene: Get Neighbor Gene

In gtexr: Query the GTEx Portal API

Get Neighbor Gene

Description

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

## Not run: 
get_neighbor_gene(pos = 1000000, chromosome = "chr1", bp_window = 10000)

## End(Not run)

gtexr documentation built on June 8, 2025, 10:26 a.m.