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:
PPvariants<-matrix(c(150,47,21,74,53,53), nrow=2,ncol=3,dimnames=list(c("disease1", "disease2"),c("downgraded", "equal", "upgraded")),
downgraded equal upgraded
disease1 150 47 21
disease2 74 53 53
Pearson's Chi-squared test
X-squared = 36.69, df = 2, p-value = 1.079e-08
Pairwise comparisons using chi-squared tests
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!!