基于字符向量将类比函数应用于列表的不同元素

Question

我有一个数据框 (subset_df)，如下所示：

structure(list(sequence = c("CSPPPPSPSPHPRPP", "GEGSPTSPTSPKQPG", 
"EAGAPAGSGAPPPAD", "PAPPKPKESKEPENA", "AKPKQQDEDPDGAAE", "AYATMLKDVQWKVRKS", 
"HEKLVQDIWKKLEAKG", "SCSVKLGLWKNAVNNC", "MAYVCELGPNQGWK", "LKDPKQYQSIVDAEWK", 
"KEAPGATEKDRAKATP", "TAYIMRPLDHGADVTL", "CVTQEHFREAMAKTNP", "AGTGFPYREMMPMNAP", 
"HKKSTEDNDDDAFCAP", "RPGGPPGYRTPYTAK", "TQGDRQKIQDAVSAA", "EVKSRYNVDVSQNKR", 
"VIEMTRAFEDDDFDK", "GSADLTPSNLTRPAS"), group = c("BP", "BP", 
"BP", "BP", "BP", "EpQ", "EpQ", "EpQ", "EpQ", "EpQ", "abc", "abc", 
"abc", "abc", "abc", "LbT", "LbT", "LbT", "LbT", "LbT")), .Names = c("sequence", 
"group"), row.names = c(NA, -20L), class = c("tbl_df", "tbl", 
"data.frame"))

最后，我想创建一个新列 (subset_df$ID)，其 ID 基于 subset_df$sequence 下的每个条目，遵循以下模式：

• group_number_subset_df$sequence 下的前四个字符。

为了说明，下面我贴几个例子：

"BP_1_CSPP"  "BP_2_GEGS"  "BP_3_EAGA"  "BP_4_PAPP"  "BP_5_AKPK"  "EpQ_1_AYAT"

我正在使用 stringr 包中的函数 str_sub 来生成输出（请参阅下面的循环）。

到目前为止，我所做的如下：

# define where the groups are (BP, abc, LbT, EpQ)
groups <- c("BP", "EpQ", "abc", "LbT")

# define the indexes of all groups using a loop
groups_indexes <- list()
for(i in groups) {
  groups_indexes[[i]] <- grep(pattern = i, x = subset_df$group)
}

考虑到我的列表 (groups_indexes) 输出：

$BP
[1] 1 2 3 4 5

$EpQ
[1]  6  7  8  9 10

$abc
[1] 11 12 13 14 15

$LbT
[1] 16 17 18 19 20

我只为groups_indexes 中的每个元素使用了一个for loop 来完成这项工作，如下所示（四个for loops）

# BP
for(i in groups_indexes[1]) {
  subset_df$IDs[i] <- paste0("BP_", i, "_", str_sub(string = subset_df$sequence[i], start = 1, end = 4))
}

# EpQ
for(i in groups_indexes[2]) {
  subset_df$IDs[i] <- paste0("EpQ_", i-(groups_indexes$EpQ[1])+1, "_", str_sub(string = subset_df$sequence[i], start = 1, end = 4))
}

# abc
for(i in groups_indexes[3]) {
  subset_df$IDs[i] <- paste0("abc_", i-(groups_indexes$abc[1])+1, "_", str_sub(string = subset_df$sequence[i], start = 1, end = 4))
}

# LbT
for(i in groups_indexes[4]) {
  subset_df$IDs[i] <- paste0("LbT_", i-(groups_indexes$LbT[1])+1, "_", str_sub(string = subset_df$sequence[i], start = 1, end = 4))
}

分别运行这四个for loops后，得到如下输出：

> subset_df$IDs
 [1] "BP_1_CSPP"  "BP_2_GEGS"  "BP_3_EAGA"  "BP_4_PAPP"  "BP_5_AKPK"  "EpQ_1_AYAT" "EpQ_2_HEKL" "EpQ_3_SCSV" "EpQ_4_MAYV" "EpQ_5_LKDP"
[11] "abc_1_KEAP" "abc_2_TAYI" "abc_3_CVTQ" "abc_4_AGTG" "abc_5_HKKS" "LbT_1_RPGG" "LbT_2_TQGD" "LbT_3_EVKS" "LbT_4_VIEM" "LbT_5_GSAD"

但是，我正在尝试使用单个循环来完成这项工作。我想使用names(groups_indexes[i]) 来调用我的for loops 中的引号中的字符（“BP”、“EpQ”、“abc”、“LbT”）。

Answer 1

也许我们需要按'group'分组，然后paste'group'与行序列（row_number()）和'sequence的子字符串（substr）

library(dplyr)
subset_df %>% 
       group_by(group) %>% 
       mutate(ID = paste(group, row_number(), substr(sequence, 1, 4), sep="_"))
#          sequence group         ID
#              <chr> <chr>      <chr>
#1   CSPPPPSPSPHPRPP    BP  BP_1_CSPP
#2   GEGSPTSPTSPKQPG    BP  BP_2_GEGS
#3   EAGAPAGSGAPPPAD    BP  BP_3_EAGA
#4   PAPPKPKESKEPENA    BP  BP_4_PAPP
#5   AKPKQQDEDPDGAAE    BP  BP_5_AKPK
#6  AYATMLKDVQWKVRKS   EpQ EpQ_1_AYAT
#7  HEKLVQDIWKKLEAKG   EpQ EpQ_2_HEKL
#8  SCSVKLGLWKNAVNNC   EpQ EpQ_3_SCSV
#9    MAYVCELGPNQGWK   EpQ EpQ_4_MAYV
#10 LKDPKQYQSIVDAEWK   EpQ EpQ_5_LKDP
#11 KEAPGATEKDRAKATP   abc abc_1_KEAP
#12 TAYIMRPLDHGADVTL   abc abc_2_TAYI
#13 CVTQEHFREAMAKTNP   abc abc_3_CVTQ
#14 AGTGFPYREMMPMNAP   abc abc_4_AGTG
#15 HKKSTEDNDDDAFCAP   abc abc_5_HKKS
#16  RPGGPPGYRTPYTAK   LbT LbT_1_RPGG
#17  TQGDRQKIQDAVSAA   LbT LbT_2_TQGD
#18  EVKSRYNVDVSQNKR   LbT LbT_3_EVKS
#19  VIEMTRAFEDDDFDK   LbT LbT_4_VIEM
#20  GSADLTPSNLTRPAS   LbT LbT_5_GSAD

如果我们的数字不是按组和基于整列的，那么删除group_by 操作就可以了

subset_df %>%
     mutate(ID = paste(group, row_number(), substr(sequence, 1, 4), sep="_"))