20

我有一个包含任何这些值的数据框。

from=c("A","C","G","T","R","Y","M","K","W", "S","N")

我想相应地替换为

to=c("AA","CC","GG","TT","AG","CT","AC","GT","AT", "CG","NN")

最好的方法是什么，循环所有要替换的值？或循环矩阵位置。或任何其他解决方案？

dd<-matrix(sample(from, 100, replace=TRUE), 10) 

dd
      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
 [1,] "K"  "S"  "G"  "T"  "R"  "N"  "A"  "C"  "W"  "M"  
 [2,] "Y"  "K"  "S"  "G"  "T"  "R"  "N"  "A"  "C"  "W"  
 [3,] "M"  "Y"  "K"  "S"  "G"  "T"  "R"  "N"  "A"  "C"  
 [4,] "W"  "M"  "Y"  "K"  "S"  "G"  "T"  "R"  "N"  "A"  
 [5,] "C"  "W"  "M"  "Y"  "K"  "S"  "G"  "T"  "R"  "N"  
 [6,] "A"  "C"  "W"  "M"  "Y"  "K"  "S"  "G"  "T"  "R"  
 [7,] "N"  "A"  "C"  "W"  "M"  "Y"  "K"  "S"  "G"  "T"  
 [8,] "R"  "N"  "A"  "C"  "W"  "M"  "Y"  "K"  "S"  "G"  
 [9,] "T"  "R"  "N"  "A"  "C"  "W"  "M"  "Y"  "K"  "S"  
[10,] "G"  "T"  "R"  "N"  "A"  "C"  "W"  "M"  "Y"  "K"

我使用了从到到的循环。

myfunc<-function(xx){

  from=c("A","C","G","T","R","Y","M","K","W", "S","N");
  to=c("AA","CC","GG","TT","AG","CT","AC","GT","AT", "CG","NN");
  for (i in 1:11){
      xx[xx==from[i]]<-to[i];
  }
  return(xx);
}

它适用于小矩阵，但对于大矩阵需要很长时间。有什么有效的解决办法吗？

谢谢

4

3 回答 3

27

创建地图

map = setNames(to, from)

然后从 A 到 B

dd[] = map[dd]

该地图用作查找，将“来自”名称与“到”值相关联。分配保留矩阵尺寸和暗名。

于 2013-04-09T20:54:00.190 回答
6 
matrix(to[match(dd,from)], nrow=nrow(dd))

match返回一个没有维度的向量，因此您需要重新创建矩阵。

于 2013-04-09T20:56:58.117 回答
3

我使用了与 OP 类似的 for 循环，并对解决方案进行计时。Theodore 的速度稍快，但 Martin 的可读性很强。

dd<-matrix(sample(from, 100, replace = TRUE),10,10)
ddr <- dd
ddm <- dd
ddt <- dd

benchmark(roman = {
  for (i in 1:length(from)) {
    ddr[ddr == from[i]] <- to[i]
  }},
  martin = {
    map = setNames(to, from)
    ddm[] = map[dd]
  },
theodore = {ddt <- matrix(to[match(dd,from)], nrow=nrow(dd))},
          replications = 100000
)
      test replications elapsed relative user.self sys.self user.child sys.child
2   martin       100000    1.93    1.191      1.91        0         NA        NA
1    roman       100000    8.23    5.080      8.11        0         NA        NA
3 theodore       100000    1.62    1.000      1.61        0         NA        NA
于 2013-04-09T21:10:29.897 回答