# Interpretation of chisq.multcomp

Hello,
I have a group of genetic variants identified in 2 different disease. I performed a reclassification of the variants and I want to determine if there is any difference in the proportion of reclassified variants between the 2 diseases. I want to be able to say, for example, in disease1 variants are more frequently reclassified and in disease1 variants are more frequently upgraded.
Data is: two samples (disease1 and disease2) with different variatns and 3 categories in the reclassification variable (downgraded, equal, upgraded).

I'm running the following code with also the results:

• ``````               byrow=TRUE)
``````

PPvariants
disease1 150 47 21
disease2 74 53 53
chisq.test(PPvariants)

``````Pearson's Chi-squared test
``````

data: PPvariants
X-squared = 36.69, df = 2, p-value = 1.079e-08

chisq.multcomp(PPvariants, p.method="fdr")

``````Pairwise comparisons using chi-squared tests
``````

data: PPvariants

``````        21      47      53      53      74
``````

47 0.00269 - - - -
53 0.00037 0.58769 - - -
53 0.00037 0.58769 1.00000 - -
74 1.6e-07 0.02116 0.07800 0.07800 -
150 < 2e-16 1.6e-12 3.7e-11 3.7e-11 9.5e-07

P value adjustment method: fdr

It will be correct to say the following conclusions?
proportion of reclassified variants is statistically different between disease1 and disease2. (chisq.test = 1.079e-08)
and: in disease1 variants are more frequently downgraded (comparison btw values 150 and 74 from chisq.multcomp = 9.5e-07) while in disease2 are more frequently upgraded (comparison btw values 21 and 53 from chisq.multcomp = 0.00037) . And proportion of variants that maintain their classification is not statistically different between disease1 and disease2

Thank you very much for your help!!

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