Question

我有以下虚拟数据帧：

structure(list(ref = structure(1:7, .Label = c("a", "b", "c", 
"d", "e", "f", "g"), class = "factor"), gene = structure(c(1L, 
1L, 1L, 1L, 1L, 2L, 2L), .Label = c("gyrA", "parC"), class = "factor"), 
    result = structure(c(2L, 4L, 6L, 2L, 3L, 5L, 1L), .Label = c("S479T", 
    "S83L", "S83L, D678E, D741E", "S83L, D87G", "T765E", "V196A, M248V, E678D"
    ), class = "factor")), class = "data.frame", row.names = c(NA, 
-7L))

看起来像这样：

ref  gene  result
a    gyrA  S83L
b    gyrA  S83L, D87G
c    gyrA  V196A, M248V, E678D
d    gyrA  S83L
e    gyrA  S83L, D678E, D741E
f    parC  T765E
g    parC  S479T

我想做的是检查“结果”列中的数值（每个条目中两个字母之间）是否在特定范围内，特别是67-106，但仅当“基因”列= = gyrA。需要检查“结果”列中每个单元格中的所有数字。如果单元格中的任何数字在指定范围内，则result_pos中的结果应返回1。我尝试了以下方法：

df %>%
   mutate(gyrA_pos = ifelse(gene == "gyrA", gsub("[[:alpha:]]", "", result), NA),
   result_pos = ifelse(gene == "gyrA" & gyrA_pos %in% as.character(seq(from = 67, to = 106)) == TRUE, 1, 0))

这有效，但仅适用于只有一个值的条目。我还发现在匹配之前必须创建一个带有字母去除的列的过程很麻烦。我最后要这样：

ref  gene  result                 result_pos
a    gyrA  S83L                   1
b    gyrA  S83L, D87G             1
c    gyrA  V196A, M248V, E678D    0
d    gyrA  S83L                   1
e    gyrA  S83L, D678E, D741E     1
f    parC  T765E                  NA
g    parC  S479T                  NA

Answer 1

这是一种方式。您可以使用str_extract_all来获取result中的所有数字，而不仅仅是第一个，然后使用map和any来检查是否有任何数字在指定范围。最后只是在需要的地方插入NA并转换为整数。

library(tidyverse)
df <- structure(list(ref = structure(1:7, .Label = c("a", "b", "c", "d", "e", "f", "g"), class = "factor"), gene = structure(c(1L, 1L, 1L, 1L, 1L, 2L, 2L), .Label = c("gyrA", "parC"), class = "factor"), result = structure(c(2L, 4L, 6L, 2L, 3L, 5L, 1L), .Label = c("S479T", "S83L", "S83L, D678E, D741E", "S83L, D87G", "T765E", "V196A, M248V, E678D"), class = "factor")), class = "data.frame", row.names = c(NA, -7L))

df %>%
  mutate(
    result_pos = result %>%
      str_extract_all("\\d+") %>%
      map(as.integer) %>%
      map_lgl(~ any(.x >= 67L & .x <= 106L)),
    result_pos = if_else(gene != "gyrA", NA, result_pos),
    result_pos = as.integer(result_pos)
  )
#>   ref gene              result result_pos
#> 1   a gyrA                S83L          1
#> 2   b gyrA          S83L, D87G          1
#> 3   c gyrA V196A, M248V, E678D          0
#> 4   d gyrA                S83L          1
#> 5   e gyrA  S83L, D678E, D741E          1
#> 6   f parC               T765E         NA
#> 7   g parC               S479T         NA

由Vue.set()（v0.2.0）于2018-09-04创建。

Answer 2

这是一个data.table选项。

library(data.table)
setDT(DF)
DF[, `:=`(result = as.character(result), # coerce result to character
          result_pos = NA_integer_)] # set result_pos to NA 
DF[gene == 'gyrA', result_pos := {
  x <-
    lapply(strsplit(result, split = ","),
           gsub,
           pattern = "\\D+",
           replacement = "")
  as.integer(sapply(x, function(i)
    any(as.numeric(i) >= 67 & as.numeric(i) <= 106)))
}][]
#   ref gene              result result_pos
#1:   a gyrA                S83L          1
#2:   b gyrA          S83L, D87G          1
#3:   c gyrA V196A, M248V, E678D          0
#4:   d gyrA                S83L          1
#5:   e gyrA  S83L, D678E, D741E          1
#6:   f parC               T765E         NA
#7:   g parC               S479T         NA

想法是strsplit列result，删除字母，检查条件并返回整数，仅针对gene == 'gyrA'行。

检查字符串中的多个值是否在数字范围R之内

2 个答案: