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

Source: R/query.R

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

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"))