xQTLquery_gene: Query basic information for genes, including name, symbol,...

In dingruofan/xQTLbiolinks: An R Package for Integrative Analysis of Quantitative Trait Locus Data of 'xQTL'

Query basic information for genes, including name, symbol, position and description

Description

Query basic information for genes, including name, symbol, position and description

Usage

xQTLquery_gene(genes = "", geneType = "auto", recordPerChunk = 100)

Arguments

genes	A charater vector or a string of gene symbol, gencode id (versioned or unversioned), or a charater string of gene type. gene symbol (Default). A character string or a character vector (case ignored). like: "tp53","naDK","SDF4". gencode/ensemble id (versioned or unversioned). A character string or a character vector (case ignored). like: "ENSG00000210195.2","ENSG00000078808". gene classification. when "geneType" is "geneCategory", supported "genes" can be listed using function gencodeGenetype$V26 or gencodeGenetype$V19
geneType	(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".
recordPerChunk	(integer) number of records fetched per request (default: 150).

Value

A data.table object of queried gene information. including following columns:

• genes. Input genes

• geneSymbol. Gene symbol.

• gencodeId. Gencode/ensemble id (versioned).

• entrezGeneId. Entrez gene ID.

• geneType. Gene type.

• chromosome. Note: "chr" is added in gencode v26,

• start.

• end.

• strand.

• tss. Transcriptional start site.

• gencodeVersion. Gencode Version.

• genomeBuild. Genome version.

• description.

Examples

# query gene of gencode version v26/hg38
geneInfo <- xQTLquery_gene("TP53")
geneInfo <- xQTLquery_gene(c("tp53","naDK","SDF4") )
geneInfo <- xQTLquery_gene(c("ENSG00000210195.2","ENSG00000078808"))

dingruofan/xQTLbiolinks documentation built on Feb. 12, 2025, 4:57 a.m.