annoGene: Annotate gene IDs according to GTF files in gencode

In AnnoProbe: Annotate the Gene Symbols for Probes in Expression Array

Annotate gene IDs according to GTF files in gencode

Description

annoGene will return a data.frame of gene information or write them to a file (csv or html format). The user should set a list of genes to be annotated, with "ENSEMBL" or "SYMBOL" style.

Usage

annoGene(IDs, ID_type, species = "human", out_file)

Arguments

IDs	a list of genes
ID_type	the type of input IDs, should be "ENSEMBL" or "SYMBOL"
species	choose human or mouse, or rat, default: human
out_file	the filename, should be ".csv" or ".html".

Value

a dataframe which columns contain genesymbol, biotypes, ensembl ids and the positions of genes

Examples

IDs <- c("DDX11L1", "MIR6859-1", "OR4G4P", "OR4F5")
ID_type = "SYMBOL"
annoGene(IDs, ID_type)

annoGene(IDs, ID_type,out_file = tempfile(fileext = ".html"))
annoGene(IDs, ID_type,out_file = tempfile(fileext = ".csv"))

AnnoProbe documentation built on Nov. 14, 2022, 9:05 a.m.