CHI SQUARE TEST IN R for SPNs bacterial data

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9.7 years ago

vungtau_dream • 0

Hi all,

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

Thanks

SNP • 2.7k views

ADD COMMENT • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by vungtau_dream • 0

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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.

ADD REPLY • link 9.7 years ago by Devon Ryan 104k

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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

ADD REPLY • link updated 2.4 years ago by Ram 43k • written 9.7 years ago by vungtau_dream • 0

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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?

ADD REPLY • link 9.7 years ago by Alex Paciorkowski 3.5k

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