I have a list of differentially expressed genes between tumor and normal samples determined from TCGA data (BRCA). I am trying to cluster the genes into related groups and determine gene annotations for each cluster. The clustering is no problem, but annotating the clusters is proving to be difficult. I have tried using the TCGA_Biolinks function TCGAanalyze_EAcomplete, however I do not know how to make sense out of the output of this function. I have followed the tcgabiolinks vignette, and made the EABarplot (I could only get this to work for the dataset provided, not for a different dataset downloaded from the gdc), however I dont know how to get access to the genes that make up the different bars in the plot. I would like to find, for instance, a set of genes that are related to T-cell activity.
Thank you, David