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I have next SNPs data.frame structure

> str(SNPs)
'data.frame':   1703 obs. of  4 variables:
 $ group: Factor w/ 2 levels "A","B": 1 1 1 1 1 1 1 1 1 1 ...
 $ rs1  : Factor w/ 3 levels "D/D","I/D","I/I": 1 1 2 3 3 2 1 1 1 1 ...
 $ rs2  : Factor w/ 3 levels "a/a","a/b","b/b": 3 3 2 3 3 2 2 3 3 2 ...
 $ rs3  : Factor w/ 3 levels "G/G","G/T","T/T": 2 1 2 1 1 3 1 1 2 1 ...
 ...other rs


> head(SNPs)
  group rs1 rs2 rs3 ...other rs
1     A D/D b/b G/T
2     A D/D b/b G/G
3     A I/D a/b G/T
4     A I/I b/b G/G
5     A I/I b/b G/G
6     A I/D a/b T/T

For example, I noticed that rs5 4b/4a and rs6 G/G in group A very often occur together (see below). In group B they very often occur together too. So I want to know - is it statistical regularity or not.

I can create table with all pairs in both groups

> SNPs$rs5_rs6 <- paste(SNPs$rs5, SNPs$rs6)
> tmp <- table(SNPs$rs5_rs6, SNPs$group)
> tmp

              A   B
  4a/4a G/G   1  20
  4b/4a G/G  31  83
  4b/4a G/T  14  51
  4b/4a T/T   1   0
  4b/4b G/G  37 106
  4b/4b G/T  35 119
  4b/4b T/T  11  31

So, now I need compare (find p-value) group A and group B: 4a/4a G/G in group A vs 4a/4a G/G in group B, 4b/4a G/G in group A vs 4b/4a G/G in group B, 4b/4a G/T in group A vs 4b/4a G/T in group B and etc. Only this pairs/

How can I do that? I need p-values for all 

> tmp

              A   B
  4a/4a G/G   1  20 - p-value?
  4b/4a G/G  31  83 - p-value?
  4b/4a G/T  14  51 - p-value?
  4b/4a T/T   1   0 - p-value?
  4b/4b G/G  37 106 - p-value?
  4b/4b G/T  35 119 - p-value?
  4b/4b T/T  11  31 - p-value?
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  • $\begingroup$ If you can restate your question in terms of explicit null and alternative hypotheses it will be much easier for people to help you determine an appropriate test to find p-values $\endgroup$
    – heathobrien
    Jul 23, 2018 at 14:41
  • $\begingroup$ @heathobrien chisq - it is my choice. Problem is not to choice test. Problem is to calculate it for pairs in tmp $\endgroup$
    – n.osennij
    Jul 23, 2018 at 15:04
  • $\begingroup$ If your question is how to apply a chisq test to the above table, the answer is chisq.test(tmp$A, tmp$B) $\endgroup$
    – heathobrien
    Jul 23, 2018 at 15:22
  • $\begingroup$ heathobrien, my question is how to apply chisq test to tmp and get 7 p-values: compare4a/4a G/G in group A vs 4a/4a G/G in group B and get first p-value, compare 4b/4a G/G in group A vs 4b/4a G/G in group B and get the second p-value and etc. $\endgroup$
    – n.osennij
    Jul 23, 2018 at 15:26
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    $\begingroup$ OK. Now we're getting somewhere. See my answer $\endgroup$
    – heathobrien
    Jul 23, 2018 at 16:01

1 Answer 1

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You can get standardised residuals from chisq.test and convert these to p-values, but it's not recommended. The frequencies of each genotype depend on the counts of all other genotypes, so the p-values aren't independent and they aren't corrected for multiple testing, but if you must: 

pnorm(-abs(chisq.test(tmp[,c('A','B')])$stdres)))
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  • $\begingroup$ hm... What other options are possible? whether the differences between the two groups were statistically significant for all pairs (rs5+rs6 and all pairs - 4a/4a G/G, 4b/4a G/G and etc)? $\endgroup$
    – n.osennij
    Jul 23, 2018 at 16:07
  • $\begingroup$ If I were you, I would just focus on the overall chisq p-value (corrected for the number of SNP pairs tested). The frequency of allele 2 depends on the frequency of allele 1 and the frequency of the genotypes depends on the allele frequencies, so I don't think it makes much sense to test each genotype independently $\endgroup$
    – heathobrien
    Jul 23, 2018 at 16:18
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    $\begingroup$ Note that all you're doing is looking at differences in linkage disequilibrium between groups. There are a lot of tools out there to that efficiently $\endgroup$
    – heathobrien
    Jul 23, 2018 at 16:41
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    $\begingroup$ Fishers exact test doesn't give you residuals. Having values less than 5 is probably the least of your worries if you're trying to obtain p-values for each combination of genotypes. $\endgroup$
    – heathobrien
    Jul 23, 2018 at 20:36
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    $\begingroup$ Let us continue this discussion in chat. $\endgroup$
    – heathobrien
    Jul 23, 2018 at 20:45

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