Fisher's exact test for Copy Number Variation association in R

Question

[taghizadehkobra]

Hi dears,

I have done CNV detection for two type tails in sheep using 50k ovine snp chip.now I need to do association test between cases(fat-tailed) and controls(thin-tail) samples. I have used the Fisher's exact test in CNVRuler softwar, but I am not sure about output accuracy ,that is why I want to exam the Fisher's test by other programs such as R or anything.

Does anyone have any suggestions?

I really would appreciate if help me

Below is the example of calling CNVs :

chr1:261243718-261310212      numsnp=3      length=66,495      state2,cn=1 baluchifinal.split11 startsnp=OAR1_261243718.1 endsnp=OAR1_261310212.1
chr11:18062193-18172161       numsnp=3      length=109,969     state2,cn=1 baluchifinal.split11 startsnp=OAR11_18062193.1 endsnp=OAR11_18172161.1

[Nicolas Rosewick]

If you can translate your data in a contingency table then it's easy to perform a fisher exact test in R.

[taghizadehkobra]

Do you have any example please?I'm beginner R user,

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

[German.M.Demidov]

That's the contingency table: https://en.wikipedia.org/wiki/Contingency_table . Fisher test works with 2x2 contingency tables only, so I think people'd like to see this table but for your data and the answer provided by CNVRuler.