[R] To Merge or to use Indicator Variables?

[oaxacamatt]

Greetings all,
I have two sets of data that I would like to investigate. The first is
gene/genome related data given different 'cell-states'. The second set of
data is relates the genes to a biological pathway. /(I think in pictures so
here goes.)/
*dataframe1*
gene, cell-state1, cell-state2
gene1, x1, y1
gene2, x2, y2
gene.x, ..., ...

*dataframe2*
pathway1, gene-x1, gene-x2, ...
pathway2, gene-y1, gene-y2, ...

What I want to do is, see if 'cell-state1' (in-)activates different genes /
pathways from 'cell-state2.' Furthermore, I would like to test for
correlation /(t-test and maybe graphing)/ between the cell-states 1 Vs 2 for
specific pathways.

My question is, which commands or method would allow me to do this most
easily/efficiently: *merge* or using *dummy variables*?

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