pairwise comparisons between pairs of proportions in R with a correction for some multiple testing rather all possible multiple testing

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Is it possible to get the multiple comparison adjustment in pairwise.prop.test() to use less than the full number of comparisons? For example, if I only care about 4 vs 1,2,3 (3 comparisons) below, I would multiply the p-values in the bottom row by 3 instead of 6 (which is the full number of pairwise comparisons) to do the Bonferroni adjustment. p.adjust has the n argument, but I can't figure out how to pass it through by doing something like

pairwise.prop.test(x=b$s,n=b$pop,p.adjust.method="bonferroni", p.adjust.n = 3, alternative="two.sided", correct = FALSE)

With Bonferroni, it's trivial, but much more involved with the other types of corrections.

Here's the result (with code below):

> b <- data.frame(
+     s=c(18,53,49,30),
+   pop=c(29,100,88,73),
+   reg=c("1","2","3","4")
+ )
> pairwise.prop.test(x=b$s,n=b$pop,p.adjust.method="none",alternative="two.sided", correct = FALSE)

    Pairwise comparisons using Pairwise comparison of proportions 

data:  b$s out of b$pop 

  1     2     3    
2 0.387 -     -    
3 0.547 0.713 -    
4 0.056 0.122 0.065

P value adjustment method: none 
> pairwise.prop.test(x=b$s,n=b$pop,p.adjust.method="bonferroni", alternative="two.sided", correct = FALSE)

    Pairwise comparisons using Pairwise comparison of proportions 

data:  b$s out of b$pop 

  1    2    3   
2 1.00 -    -   
3 1.00 1.00 -   
4 0.33 0.73 0.39

P value adjustment method: bonferroni

Code:

b <- data.frame(
    s=c(18,53,49,30),
  pop=c(29,100,88,73),
  reg=c("1","2","3","4")
)
pairwise.prop.test(x=b$s,n=b$pop,p.adjust.method="none",alternative="two.sided", correct = FALSE)
pairwise.prop.test(x=b$s,n=b$pop,p.adjust.method="bonferroni", alternative="two.sided", correct = FALSE)
r
1 Answers

Based on @27 ϕ 9's comment:

b <- data.frame(
    s=c(18,53,49,30),
    pop=c(29,100,88,73),
    reg=c("1","2","3","4")
)
unadj <- pairwise.prop.test(x=b$s,n=b$pop,p.adjust.method="none",alternative="two.sided")
p.adjust(unadj$p.value[3, ], method = "holm") 
pairwise.prop.test(x=b$s,n=b$pop,p.adjust.method="bonferroni", alternative="two.sided")
user_11876710
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