gtexr (version 0.2.1)

get_neighbor_gene: 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
)

Value

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

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

See Also

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

Examples

if (FALSE) { # identical(Sys.getenv("IN_PKGDOWN"), "true")
get_neighbor_gene(pos = 1000000, chromosome = "chr1", bp_window = 10000)
}