convertGeneID: Convert gene ids according to the gene type

In NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Description

Convert gene ids according to the gene type

Usage

convertGeneID(
  genetype = c("Entrez", "mirna", "Ensembl_gene", "Ensembl_trans", "NCBI"),
  genelist,
  org_assembly = c("hg19", "hg38", "mm10", "dre10", "rn6", "dm6", "ce11", "sc3")
)

Arguments

genetype	Type of the input gene list. Possible values are "Entrez", "mirna", "Ensembl_gene", "Ensembl_trans", "NCBI". For HUGO gene symbol "NCBI" value, for Entrez gene id "Entrez", for mirbase id "mirna" is used.
genelist	Input gene list
org_assembly	Genome assembly of interest for the analysis. Possible assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and "hg38" for human

Value

GRange object of the given input

Examples

convGene <-convertGeneID(genetype = "mirna",
                         genelist = brain_mirna[1:30,],
                         org_assembly = 'hg19')

NoRCE documentation built on Nov. 8, 2020, 7:17 p.m.