annoGene {AnnoProbe}

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"))