Question

我想扩展compare multiple vectors of different lengths, count the elements that are the same, and print out those that are the same and different的工作范围。我想编写一个循环，以便可以对所有10种不同的向量进行成对比较，以找出每种比较中所有可能的成对选择所共有的向量。下面的伪代码的主要比较部分正在工作，并且来自上一篇文章，但这只是比较A和B，我想将A与C，A与＃D，B与C等进行比较。 ..

vectors to be compared: A, B, C, D, E, F, G, H, I, J
set global variable for first vector to be compared
set global variable for second vector to be compared

#vetors -- these are subsets of my real vectors, which are more like 50 - 200 elements long
A <- c("866_78", "1137_78", "1721_78", "1745_79", "1910_79", "1972_76", 
        "2776_77",  "3049_79", "3084_15",  "3995_78", "4066_33", "4431_15")
B <- c("866_78", "1137_78", "1721_78", "1745_79", "1910_79", "1972_76", 
       "2776_77",  
       "3049_79", "3084_15",  "3995_78")
C <- c("866_78", "1137_78", "1910_79", "1972_76", "2776_77",  
       "3049_79", "3084_14",  "3995_78", "4066_36", "4431_19", "4885_78")
D <- c("866_78", "1137_78", "1721_78", "1745_79", "1910_79", "1972_76", 
      "2773_77",  
       "3049_79", "3084_12",  "3995_78", "4066_36", "4431_19", "4885_78")
E <- c("866_78", "1137_78", "1721_78", "1745_79", "1910_79", "1972_76", 
      "2776_77",  
       "3049_79", "3084_17", "4431_19", "4885_78")
F <- c("868_78", "1137_78", "1721_78", "1745_79", "1910_79", "1972_76", 
       "2776_77",  
       "3049_79", "3084_15",  "3995_78", "4066_36", "4431_19", "4885_78")
G <- c("866_78", "1837_78", "1721_78", "1972_76", "2776_77",  
       "3049_79", "3084_15",  "3995_78", "4066_36", "4431_19", "4885_78")
H <- c("866_78", "1137_78", "1721_78", "1745_79", "1910_79", "1972_76", 
        "2776_77",  
       "3049_79", "3084_15",  "3995_78", "4066_36", "4431_19", "4885_78")
I <- c("866_78", "1137_28", "1721_78", "1745_79", "1910_79", "1972_76", 
       "2776_77",  
       "3995_78", "4066_36", "4431_19", "4885_78")
J <- c("866_78", "1137_78", "1721_78", "1745_79", "1910_79", "1972_76", 
       "2776_77",  
       "3049_79", "3084_18",  "3995_78", "4066_36", "4431_19", "4885_78")

for(i ???)
{
compare.SNPs <- function(A, B) {
  # consider only unique names
  A.u <- unique(A)
  B.u <- unique(B)
  common.A.B <- intersect(A.u, B.u)
  diff.A.B <- setdiff(A.u, B.u)
  diff.B.A <- setdiff(B.u, A.u)
  uncommon.A.B <- union(diff.A.B, diff.B.A)
  cat(paste0("The sets have ", length(common.A.B), " SNPs in common:"))
  print(common.A.B)
  print(paste0("The sets have ", length(uncommon.A.B), " SNPs not in 
  common:"))
  print(paste0("In the first set, but not in the second set:"))
  print(diff.A.B)
  print(paste0("Not in the first set, but in the second set:"))
  print(diff.B.A)

}
compare.SNPs(A,B)
}

对于示例代码的任何指导，将不胜感激。

此致，埃拉

Answer 1

xx<-combn(LETTERS[1:10],2)
for (i in 1:dim(xx)[2]) {
      cat(paste0("Comparing ", xx[1,i], " and ", xx[2,i],": "))
      compare.SNPs(get(xx[1,i]),get(xx[2,i]))
    }

（而且，function()调用没有理由位于for循环内）。

Answer 2

首先，您应该告诉函数compare.SNPs在return中给您一些东西，而不仅仅是打印。这是通过return(list(common.A.B, diff.A.B, diff.B.A))

完成的

compare.SNPs <- function(A, B) {
  # consider only unique names
  A.u <- unique(A)
  B.u <- unique(B)
  common.A.B <- intersect(A.u, B.u)
  diff.A.B <- setdiff(A.u, B.u)
  diff.B.A <- setdiff(B.u, A.u)
  uncommon.A.B <- union(diff.A.B, diff.B.A)
  cat(paste0("The sets have ", length(common.A.B), " SNPs in common:"))
  print(common.A.B)
  print(paste0("The sets have ", length(uncommon.A.B), " SNPs not in 
               common:"))
  print(paste0("In the first set, but not in the second set:"))
  print(diff.A.B)
  print(paste0("Not in the first set, but in the second set:"))
  print(diff.B.A)
  return(list(common.A.B, diff.A.B, diff.B.A))
}

所以现在此函数将return变成list，其中包含3个元素：两个向量的公共元素，然后是2组差异。

mylist <- list(A, B, C, D, E, F, G, H, I, J)
allcomparisons <- list()
for(i in 1:length(mylist))
{
  for(j in 1:length(mylist)) {
    allcomparisons <- c(allcomparisons, compare.SNPs(mylist[[i]], mylist[[j]]))
  }
}

比较A与J比较10x10个元素，总共可以得到300个元素：首先是A和A的共同元素，然后是A和A之间的区别，然后是A和A之间的区别，然后是共同元素A和B等。然后，您可以像访问其他列表一样访问allcomparisons的元素。例如，您可以检查all(allcomparisons[[4]]==compare.SNPs(A,B)[[1]])

[1] TRUE

比较不同长度的多个向量

2 个答案: