r - 连接整个数据框的列对

Question

我正在处理遗传数据，我需要连接成对的列。我拥有的数据在不同的列中有主要和次要等位基因(例如，等位基因 1a、等位基因 1b、等位基因 2a、等位基因 2b 等)。我需要一种方法来为整个数据框成对列。我在下面包含了一个示例，但我的数据有 170 万对(所以我现在有 340 万列)，所以如果我需要为每一列命名，它将无法工作。稍后我将更改列名。如果在 R 中有一种方法可以做到这一点，我们将不胜感激。I have tried to create a sequence and paste them ，类似:

df <- data.frame(id = seq(1,20),
                 var1 = rep("A", 20),
                 var2 = c(rep("T", 10), rep("A", 10)),
                 var3 = rep("C", 20),
                 var4 = c(rep("C", 10), rep("G", 10)),
                 var5 = rep("A", 20),
                 var6 = c(rep("A", 10), rep("G", 10)),
                 stringsAsFactors = FALSE)

i <- seq.int(1, length(ped), by = 2L)
df <- paste0(df[i], df[i+1])

但这没有用。我希望它来自:

    id var1 var2 var3 var4 var5 var6
1   1    A    T    C    C    A    A
2   2    A    T    C    C    A    A
3   3    A    T    C    C    A    A
4   4    A    T    C    C    A    A
5   5    A    T    C    C    A    A
6   6    A    T    C    C    A    A
7   7    A    T    C    C    A    A
8   8    A    T    C    C    A    A
9   9    A    T    C    C    A    A
10 10    A    T    C    C    A    A
11 11    A    A    C    G    A    G
12 12    A    A    C    G    A    G
13 13    A    A    C    G    A    G
14 14    A    A    C    G    A    G
15 15    A    A    C    G    A    G
16 16    A    A    C    G    A    G
17 17    A    A    C    G    A    G
18 18    A    A    C    G    A    G
19 19    A    A    C    G    A    G
20 20    A    A    C    G    A    G

到:

   id var1 var2 var3
1   1   AT   CC   AA
2   2   AT   CC   AA
3   3   AT   CC   AA
4   4   AT   CC   AA
5   5   AT   CC   AA
6   6   AT   CC   AA
7   7   AT   CC   AA
8   8   AT   CC   AA
9   9   AT   CC   AA
10 10   AT   CC   AA
11 11   AA   CG   AG
12 12   AA   CG   AG
13 13   AA   CG   AG
14 14   AA   CG   AG
15 15   AA   CG   AG
16 16   AA   CG   AG
17 17   AA   CG   AG
18 18   AA   CG   AG
19 19   AA   CG   AG
20 20   AA   CG   AG

编辑:谢谢!!!我能够为我的数据调整两个答案，@akrun 跑得更快了。我创建了一个包含 100 行和 100,000 列的数据子集，结果如下:

microbenchmark(
+   {
+   new <- ped %>%
+   gather(key = V, value = value, -id) %>%
+   mutate(V = str_extract(V, "\\d+") %>% as.numeric()) %>%
+   group_by(id) %>%
+   mutate(pair = ceiling(V / 2)) %>% 
+   group_by(id, pair) %>%
+   summarise(combined = paste(value, collapse = "")) %>%
+   mutate(V_combo = paste0("V", pair)) %>%
+   select(-pair) %>%
+   spread(key = V_combo, value = combined) %>%
+   select(id, paste0("V", seq(1, ncol(.)-1, 1)))
+   },
+   {
+   out <- ped[1]
+   new_cols <- paste0("V", seq(1, (ncol(ped)-1)/2))
+   
+   out[new_cols] <- lapply(seq(2, ncol(ped)-1, 2), 
+                           function(i) do.call(paste0, ped[i:(i+1)]))
+   },
+   times = 1
+   )

Unit: seconds                                                                                                                                                                                                                                                                                                                                                                                                                                               

   expr           min        lq      mean    median        uq       max neval
camille     250.30901 250.30901 250.30901 250.30901 250.30901 250.30901     1
akrun       23.52434  23.52434  23.52434  23.52434  23.52434  23.52434     1
    > 
    > new <- data.frame(new, stringsAsFactors = FALSE)
    > identical(new, out)
    [1] TRUE

Answer 1

我们可以创建一个循环来对列和相邻列进行子集化，paste 将其 withdo.call` 并将其作为新列分配给新数据集

out <- df[1]
out[paste0("var", 1:3)] <- lapply(seq(2, ncol(df), 2), 
               function(i) do.call(paste0, df[i:(i+1)]))