Convert ensembl IDs from dataframe to entrez IDs vector

Question

[alyyha]

I want to convert ensembl IDs in to entrez IDs to perform Ontology Analysis. I need to create a vector of ensembl IDs and it does not work.

library(ChIPpeakAnno) #to use the function convert2EntrezID

library(BSgenome.Athaliana.TAIR.TAIR9) #to get the entrez IDs

#I have a dataframe df of 2 columns: GENE_ID (ensembl IDs) and LFCs.

genes<-df$GENE_ID #to get a vector of gene ids
orgAnn<-BSgenome.Athaliana.TAIR.TAIR9

convert2EntrezID(genes, orgAnn, ID_type="ensembl_gene_id")

Error in as.character.default(x) : 
  no method for coercing this S4 class to a vector

[rpolicastro]

gene_ID should be genes in your function.

[alyyha]

Yes sorry I wrote wrongly here

[jv]

are you sure that BSgenome.Athaliana.TAIR.TAIR9 is compatible for use as the orgAnn for convert2EntrezID?

[alyyha]

Good point. I wanted to use a standard annotation dataset from Bioconductor, just to see if this converting function was working or not. Where would you recommend to download this annotation dataset?

[rpolicastro]

You probably want to use the A. thaliana bioconductor organism database. BSgenome objects are usually just the genome assembly, whereas organism databases have collections of useful things like various gene name formats and ontologies.

http://bioconductor.org/packages/release/data/annotation/html/org.At.tair.db.html

[alyyha]

Upsi. Thank you, I will try that