Question

我的数据框df如下所示：

structure(list(sequence = c("CSPPPPSPSPHPRPP", "GEGSPTSPTSPKQPG", 
"EAGAPAGSGAPPPAD", "PAPPKPKESKEPENA", "AKPKQQDEDPDGAAE", "GDRGGGTGNEDDDYE"
), group = c("BP", "BP", "BP", "BP", "BP", "BP")), .Names = c("sequence", 
"group"), row.names = c(NA, -6L), class = c("tbl_df", "tbl", 
"data.frame"))

对于df$sequence下的所有字符变量，我希望获得7个字符的所有可能子集，每次迭代后将一个字符向右移动。为此，我创建了一个名为scan_core_OLpeptides的函数。如果我应用以下功能：

scan_core_OLpeptides <- function(x) {
  for(i in seq_len(nchar(x)-7+1)){
    print(str_sub(string = x, start = i, end = i+6))
}}

我得到以下输出：

[1] "CSPPPPS" "GEGSPTS" "EAGAPAG" "PAPPKPK" "AKPKQQD" "GDRGGGT"
[1] "SPPPPSP" "EGSPTSP" "AGAPAGS" "APPKPKE" "KPKQQDE" "DRGGGTG"
[1] "PPPPSPS" "GSPTSPT" "GAPAGSG" "PPKPKES" "PKQQDED" "RGGGTGN"
[1] "PPPSPSP" "SPTSPTS" "APAGSGA" "PKPKESK" "KQQDEDP" "GGGTGNE"
[1] "PPSPSPH" "PTSPTSP" "PAGSGAP" "KPKESKE" "QQDEDPD" "GGTGNED"
[1] "PSPSPHP" "TSPTSPK" "AGSGAPP" "PKESKEP" "QDEDPDG" "GTGNEDD"
[1] "SPSPHPR" "SPTSPKQ" "GSGAPPP" "KESKEPE" "DEDPDGA" "TGNEDDD"
[1] "PSPHPRP" "PTSPKQP" "SGAPPPA" "ESKEPEN" "EDPDGAA" "GNEDDDY"
[1] "SPHPRPP" "TSPKQPG" "GAPPPAD" "SKEPENA" "DPDGAAE" "NEDDDYE"

这正是我想要的。但是，我想将此输出存储到一个对象中，最好是存储到矢量中或存储到data.frame中。我考虑过存储到列表中，但它没有用。

Answer 1

我会使用zoo包，

library(zoo)
sapply(strsplit(df1$sequence, ''), function(i) rollapply(i, 7, by = 1, 
                                                   function(i)paste0(i, collapse = '')))

Answer 2

我们可以修改功能以创建list来存储来自每个＆＃39;

的输出

scan_core_OLpeptides <- function(x) {
  x1 <-  vector("list", nrow(df))
  for(i in seq(nchar(x) - 7 +1) ){
   x1[[i]] <- str_sub(string = x, start = i, end = i+6)

  }
   x1
}  


scan_core_OLpeptides(df$sequence)
#[[1]]
#[1] "CSPPPPS" "GEGSPTS" "EAGAPAG" "PAPPKPK" "AKPKQQD" "GDRGGGT"

#[[2]]
#[1] "SPPPPSP" "EGSPTSP" "AGAPAGS" "APPKPKE" "KPKQQDE" "DRGGGTG"

#[[3]]
#[1] "PPPPSPS" "GSPTSPT" "GAPAGSG" "PPKPKES" "PKQQDED" "RGGGTGN"

#[[4]]
#[1] "PPPSPSP" "SPTSPTS" "APAGSGA" "PKPKESK" "KQQDEDP" "GGGTGNE"

#[[5]]
#[1] "PPSPSPH" "PTSPTSP" "PAGSGAP" "KPKESKE" "QQDEDPD" "GGTGNED"

#[[6]]
#[1] "PSPSPHP" "TSPTSPK" "AGSGAPP" "PKESKEP" "QDEDPDG" "GTGNEDD"

将函数内部的循环输出存储到vector或data.frame中

2 个答案: