Dear all,

please would you let me know, is there a package in R/BioC that has implemented randomization/permutation tests for joint genomic analyses (for example when jointly considering both GENE EXPRESSION and PROTEIN BINDING).

I know that regioneR has implemented the permutation tests to assess the spatial relations between these region sets (https://bioconductor.org/packages/release/bioc/html/regioneR.html). The context of my question is the following :

let's consider 1000 UP_REGULATED genes with increased PROTEIN X and HISTONE MARK Y (on the gene promoters or on the gene enhancers):

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

-- 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