a package with randomization/permutation tests for genomic analyses

Dear all,

please would you let me know, is there a package in R that has
implemented randomization/permutation
tests for joint genomic analyses

(an example of joint genomic analyses -- when jointly considering both GENE
EXPRESSION and PROTEIN BINDING along the DNA).

The context of my question is the following :

let's consider 1000 UP_REGULATED genes with increased PROTEIN X and with a
HISTONE MARK Y :

in order to show that PROTEIN X is related to HISTONE MARK Y for 1000
UP-regulated genes, what "controls" would you use for the comparison :

-- 1000 RANDOM GENES (and multiple randomization tests)

-- 1000 UP-REG GENES with NO PROTEIN X, NO HISTONE MARK Y

-- 1000 UP-REG GENES with PROTEIN X, and NO HISTONE MARK Y

-- 1000 UP-REG GENES with NO PROTEIN X, and with HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with NO PROTEIN X, NO HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with PROTEIN X, and NO HISTONE MARK Y

-- 1000 NOT-UP-REG GENES with NO PROTEIN X, and with HISTONE MARK Y

-- anything else ?

thanks a lot,

bogdan

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