pairwise.wilcox.test - 重新格式化输出

Question

这是测试的正常输出:

attach(airquality)
pw <- pairwise.wilcox.test(Ozone, Month, p.adj = "bonf")
pw

data:  Ozone and Month 

     May    Jun    Jul    Aug   
Jun 1.0000 -      -      -     
Jul 0.0003 0.1414 -      -     
Aug 0.0012 0.2591 1.0000 -     
Sep 1.0000 1.0000 0.0074 0.0325

我最近不得不用10个级别的因子进行测试.虽然pairwise.wilcox.test的下三角形格式是有用和简洁的,但我认为以类似的方式将它安排到Tukey HSD输出中是很方便的,其中列出每个成对组合以及它的相关p值.这是我尝试这样做的:

pw.df <- as.data.frame(pw$p.value)
pw.diff <- vector("character")
pw.pval <- vector("numeric")
for (i in 1:ncol(pw.df) )
  for (j in i:length(pw.df) ) {
    pw.diff <- c(pw.diff,paste(colnames(pw.df[i]),"-",rownames(pw.df)[j]))
    pw.pval <- c(pw.pval,pw.df[j,i])
  }


# order them by ascending p value
v <- order(pw.pval,decreasing = F)
pw.df <- data.frame(pw.diff[v],pw.pval[v])


# display those that are significant at the 5% level
pw.df[pw.df$pw.pval<0.05,]

  pw.diff.v.  pw.pval.v.
1  May - Jul 0.000299639
2  May - Aug 0.001208078
3  Jul - Sep 0.007442604
4  Aug - Sep 0.032479550

如果有人有关于如何使这更容易和/或更优雅的一些提示/技巧/建议,我将不胜感激.

Answer 1

我会使用reshape或reshape2包来完成这项任务,特别是melt()命令.pairwise.wilcox.test返回的对象包含第三个插槽中感兴趣的数据,所以melt(pw[[3]])应该这样做:

    X1  X2       value
1  Jun May 1.000000000
2  Jul May 0.000299639
3  Aug May 0.001208078
4  Sep May 1.000000000
5  Jun Jun          NA
....