Making a Group Tree using RNA-seq Read Count in R

Question

[Simon Ahn]

Hi. I'm struggling with making group tree.

The data format looks like this:

# Genes    Group A .  Group B .  Group C .  Group D
# gene A      15        20         30         20 
# gene B      0         3          20         10 
# gene C      1         7          40         20
# ... 

So I want to use hierarchical clustering method to divide those group.

Is there any packages or any method to do this in R?

Answer 1

[Biogeek]

Hi Minuate,

Can you please specify what sort of 'tree'? Do you mean a heatmap or dendrogram based figure? If so you can use heatmap.2 or pheatmap in R. In conjunction with ggplots2 and other various R modules, you can make some pretty nice diagrams.

If that count data is normalised, you can log2 the counts and use them for input into heatmap.2. I recommend Z-scaling too. Please read up on those packages and Google them, if you haven't done so already. You will be able to find some good examples on the internet.