Question: CHI SQUARE TEST IN R for SPNs bacterial data
0
gravatar for vungtau_dream
4.5 years ago by
Australia
vungtau_dream0 wrote:

Hi all,

 

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

 

Thanks

snp • 1.5k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 4.5 years ago by vungtau_dream0
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 REPLYlink written 4.5 years ago by Devon Ryan88k

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 REPLYlink written 4.5 years ago by vungtau_dream0
1

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 REPLYlink written 4.5 years ago by Alex Paciorkowski3.3k
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