根据来自另一个变量 R 的位置替换字符串中的字符

Question

我有以下数据框 xo。对于每一行，我想依次查找并替换 position_of_Ns_to_remove 中列出的位置。示例中的结果新变量应该是删除所有 R 的序列。在这种情况下，我无法根据角色本身进行搜索 - 它必须基于角色的位置。

p <- data.frame(locus = c("1","2","3"), positions_of_Ns_to_remove = c("12,17,43,100","30,60,61,62",NA))
x <- data.frame(locus = c("1","1","2","3"), sequence = c("xxxxxxxxxxxRxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxR","xxxxxxxxxxxRxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxR","xxxxxxxxxxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxRRRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx","xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"))
xo <- merge(x, p, by = c("locus"), all.x = T)

> xo
  locus                                                                                             sequence positions_of_Ns_to_remove
1     1 xxxxxxxxxxxRxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxR              12,17,43,100
2     1 xxxxxxxxxxxRxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxR              12,17,43,100
3     2 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxRRRxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx               30,60,61,62
4     3 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx                      <NA>

这在 xo 中只有 1 行时有效，但在有多行时无效。我想使用 tidyverse 函数/管道并尽可能避免循环。

  xo %>% dplyr::mutate(new_sequence = paste(
                                                    replace( unlist(strsplit(sequence, "")), as.integer(unlist(strsplit(positions_of_Ns_to_remove,","))), "" ), 
                                                   collapse = "")
                             )

我想要什么：

  locus                                                                                             new_sequence positions_of_Ns_to_remove
1     1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx              12,17,43,100
2     1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx              12,17,43,100
3     2 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx               30,60,61,62
4     3 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx                      <NA>

Answer 1

您可以构建一个自定义函数并将其应用于您的数据：

library(stringr)

# cuts the n-th character out of the string
remove_pos <- function(string, n) {
  n <- as.integer(n)
  n <- n[order(n, decreasing = TRUE)]
  len <- nchar(string)
  
  output <- string
  
  for (i in n) {
    
    output <- paste0(
      str_sub(output, start = 1L, end = i - 1L),
      str_sub(output, start = i + 1, end = len)
      )
  }
  
  return(output)
  
}

xo %>% 
  mutate(positions = str_split(positions_of_Ns_to_remove, ",")) %>% 
  group_by(locus, n=row_number()) %>%
  mutate(
    new_seq = ifelse(!is.na(positions_of_Ns_to_remove), 
                     remove_pos(sequence, unlist(positions)), 
                     sequence)
    ) %>% 
  select(-positions) %>% 
  ungroup()

返回

# A tibble: 5 x 4
  locus sequence                                    positions_of_Ns_to~ new_seq                                  
  <chr> <chr>                                       <chr>               <chr>                                    
1 1     xxxxxxxxxxxRxxxxRxxxxxxxxxxxxxxxxxxxxxxxxx~ 12,17,43,100        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx~
2 1     xxxxxxxxxxxRxxxxRxxxxxxxxxxxxxxxxxxxxxxxxx~ 12,17,43,100        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx~
3 2     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxRxxxxxxxxxxxx~ 30,60,61,62         xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx~
4 3     Rxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx~ 1                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx~
5 4     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx~ NA                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx~