Annotating ENS codes to gene name

Question

[Yoosef]

Hello. After Normalization, I have calculated DEGs using Deseq2 in R. I have reached to an excel file which only contains the transcript codes that should be translated to gene names. I would be pleased If you introduce me proper method in R to annotate my results.

 ENS                    baseMean        log2FoldChange    lfcSE         stat        pvalue            padj
ENSG00000290825.1   6.767523298 2.498149837 1.244047975 2.008081592 0.044634622 0.999989155
ENSG00000227232.5   285.893477  0.252898447 0.227415944 1.112052401 0.266115621 0.999989155
ENSG00000278267.1   15.54688642 0.463918457 0.582522804 0.796395357 0.425802276 0.999989155

[GenoMax]

This is a FAQ, Some past threads linked here: Ensembl ID to Gene Symbol Converter

Answer 1

[Apex92]

You can either use biomart to download all gene ids and gene names and then intersect them with your current table. Or you can use your annotation file (gtf) and make a two-column table that contains gene ids and gene names then intersect this table with your result.

[Yoosef]

Thank for your points. I created a data frame from my .gtf file using rtracklayer package. Can you please tell the command I should use in order to intersect my results with this table. I mean it should fill the gene name in front of my ENS codes automatically.

[Apex92]

you can use merge function in R to do this. It is quite straight forward.