R help - Mar 2020 - 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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I believe that a much better place to ask this is on the Bioconductor
Support Site:

https://support.bioconductor.org/

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Wed, Mar 4, 2020 at 9:51 PM Bogdan Tanasa <tanasa at gmail.com> wrote:
> 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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>
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