BiomaRt

Aim: To obtain a gene annotation table from the expression matrix.

To do this, we need two things:

• Access the Ensembl database
• Choose the information we want to retrieve

→ This corresponds to two steps in R and therefore two functions to know

Database selection

Associated R function : useEnsembl

dataset selection, argument : biomart

genome selection : dataset

To find out what values to set for the various parameters, you can use the following functions:

• Argument biomart → listEnsembl
• Argument dataset → listDatasets

Annotation table generation

Associated R function : getBM with attributes parameters to select categories and filter/value to retrieve only rows of interest