get_hgnc: Get hgnc symbol

In isglobal-brge/EDY: Analysis of extreme downregulation of chromosome Y (EDY)

Description

Obtaining HUGO gene nomenclature committee (hgnc) symbol from genBank accession numbers, entrezgenes (NCBI gene IDs), RefSeq IDs, UniProt IDs or Ensembl stable IDs.

Usage

get_hgnc(x, key.type, key.col, ...)

Arguments

x	An ExpressionSet, a RangedSummarizedExperiment or a vector of IDs.
key.type	A string indicating the type of gene ID that we want to get hgnc symbol from. It must be one of refseq, uniprot, ensembl, entrezgene or genbank.
key.col	A string indicating the name of the column that contains the key.type in the table of features of the ExpressionSet (accessed by fData) or in the metadata of the rows in the RangedSummarizedExperiment (accessed by rowData).

Value

In case x is a vector, the output is another vector with the hgnc symbols and the query IDs as names. Otherwise, the output is an ExpressionSet or RangedSummarizedExperiment containing the previous information in x plus the column hgnc_symbol containing the gene symbols.

isglobal-brge/EDY documentation built on Jan. 24, 2020, 3:21 a.m.