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CHI SQUARE TEST IN R for SPNs bacterial data

Hi all,

Could somone show me How I perform a chi square test in R on 40,00 SNPs data?

Thanks

snp
• 3,418 views • link
updated by Ram Ram • written by vungtau_dream • vungtau_dream 
help(apply)
help(chisq.test)

Aside from that, we'd need to know more details (e.g., what's your data look like) to give you any further help.

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written by Devon Ryan Devon Ryan

Hi there

One data contains 50000 SNPS with positions and other set of data with outcomes of drug resistance ( resistant or sensitive) . I want to do basic chi square test for each of these SNPS in R.

Thanks

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updated by Ram Ram • written by vungtau_dream • vungtau_dream

So you want to evaluate for the association of each SNP with drug resistance or sensitivity? What is your null hypothesis? That a given SNP is not associated with resistance? I think you need to be still more detailed. Is your question about chi-squared and how to frame your hypothesis, organize your data, or is your question about the R syntax? What have you tried?

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written by Alex Paciorkowski Alex Paciorkowski

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