如果没有统计差异，则覆盖 cldList 停止

Question

我正在尝试将 cld 添加到我的数据中，但 cldList 在遇到统计差异时停止工作。我的数据包含有统计差异和无统计差异的组，因此我需要一种方法来解决此问题。 cldList 是 rcompanion 包的一部分，写法如下：

cldList = function(formula = NULL,
                   data = NULL, 
                   comparison = NULL, 
                   p.value = NULL, 
                   threshold = 0.05,
                   print.comp = FALSE,
                   remove.space = TRUE,
                   remove.equal = TRUE,
                   remove.zero = TRUE,
                   swap.colon = TRUE,
                   swap.vs = FALSE,
                    ...)
  {
    if(!is.null(formula)){
      p.value     = eval(parse(text=paste0("data","$",all.vars(formula[[2]])[1])))
      comparison  = eval(parse(text=paste0("data","$",all.vars(formula[[3]])[1])))
    }
    Comparison = (as.numeric(p.value) <= threshold)
    
    if (sum(Comparison) == 0){stop("No significant differences.", call.=FALSE)}         # THIS LINE HERE #
    
    if(remove.space == TRUE) {comparison = gsub(" ",  "",  comparison)}
    if(remove.equal == TRUE) {comparison = gsub("=",  "",  comparison)}
    if(remove.zero  == TRUE) {comparison = gsub("0",  "",  comparison)}
    if(swap.colon   == TRUE) {comparison = gsub(":",  "-", comparison)}
    if(swap.vs      == TRUE) {comparison = gsub("vs", "-", comparison)}
    
    names(Comparison) = comparison
    
    if(print.comp == TRUE) 
    {Y = data.frame(Comparisons = names(Comparison), 
                    p.value = p.value, Value=Comparison,
                    Threshold=threshold)
    cat("\n", "\n")
    print(Y)
    cat("\n", "\n")}
    
    MCL = multcompLetters(Comparison, ...)
    
    Group      = names(MCL$Letters)
    Letter     = as.character(MCL$Letters)
    MonoLetter = as.character(MCL$monospacedLetters)
    
    Z = data.frame(Group, Letter, MonoLetter)
    
    return(Z)
  }

这是我的一部分数据（从另一个程序输出）：

dummy_df <-data.frame(target = c("A1","A1","A1","A1","A1","A1","A2","A2","A2","A2","A2","A2","A3","A3","A3","A3","A3","A3","A4","A4","A4","A4","A4","A4"),
                      comparison = c("a - b","a - c","a - d","b - c","b - d","c - d","a - b","a - c","a - d","b - c","b - d","c - d","e - c","e - d","e - f","c - d","c - f","d - f","e - c","e - d","e - f","c - d","c - f","d - f"),
                      significant = c("Yes","No","Yes","Yes","Yes","Yes","Yes","No","Yes","Yes","Yes","Yes","Yes","Yes","Yes","No","Yes","Yes","No","No","No","No","No","No"),
                      p.val = c( 0.04,0.06,0.04,0.04,0.04,0.04,0.04,0.06,0.04,0.04,0.04,0.04,0.04,0.04,0.04,0.06,0.04,0.04,0.06,0.06,0.06,0.06,0.06,0.06))

我的代码是这样的

i <- 1
targets <- data.frame(Genes = unique(dummy_df$target))
df <- data.frame()
df1 <- data.frame(Group = "No", Letter ="significant", MonoLetter = "differences")
 
while (i<=nrow(targets)) {
print(i)
df2 <-cldList(p.val~comparison, data = subset.data.frame(dummy_df, dummy_df$target==targets[i,]), threshold = 0.05)
   print(df2)
    
    df2$target <- targets[i,]
    #print(df2)
    
    df <- rbind(df, df2)
    
     i <- i+1
  }

我尝试在 cldList 步骤之后添加 if (nrow(df2)==0) {df2 <- df1} 以至少了解哪些目标在统计上没有差异，但没有成功。

是否有使循环继续遍历所有目标的解决方法？理想情况下，所有组的 cldList 输出具有相同的字母将是目标。

Answer 1

我是 cldList() 函数的作者。

很遗憾，您提供的循环代码对我不起作用。

但是，如果没有显着差异，我可以解决 cldList() 的行为。问题是函数所依赖的 multcompLetters 在没有显着差异时具有不同的输出。

编辑： rcompanion 包中的函数已更新为 return 具有相同字母的数据框当没有显着差异时，所有组。 (rcompanion v. 2.4.13, CRAN.R-project.org/package=rcompanion

#### Examples

library(rcompanion)

Comparison = c("A-B", "A-C", "B-C")
Pvalue     = c(0.04, 1, 1)
DataFrame  = data.frame(Comparison, Pvalue)

cldList(Pvalue ~ Comparison, data=DataFrame)

### Group Letter MonoLetter
### 1     A      a         a 
### 2     B      b          b
### 3     C     ab         ab

Comparison2 = c("A-B", "A-C", "B-C")
Pvalue2     = c(1, 1, 1)
DataFrame2  = data.frame(Comparison2, Pvalue2)

cldList(Pvalue2 ~ Comparison2, data=DataFrame2)

### Group Letter MonoLetter
### 1     A      a          a
### 2     B      a          a
### 3     C      a          a

如果没有统计差异，则覆盖 cldList 停止

Override cldList stop if no statistical differences

statistics

loops

r