Store the output of a loop inside a function into a vector or data.frame

Question

I have a data frame df that looks like the following:

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"))

For all the character variables underdf$sequence I want to get all the possible sub-sets of 7 characters, shifting one character to the right after each iteration. For that, I created a function called scan_core_OLpeptides. If I apply the following function:

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

I get the following output:

[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"

Which is exactly what I want. However, I wanted to store this output into an object, preferably into a vector or into a data.frame. I thought about storing into a list but it did not work.

You can use apply to get it int to an object or create an object in for loop and pass the output to that — akrun
– akrun, Commented Mar 31, 2017 at 14:23
I tried to create the object and store each iteration into it, yet it did not work. — BCArg
– BCArg, Commented Mar 31, 2017 at 14:30

Sotos · Accepted Answer · 2017-03-31 14:23:33Z

3

I 'd use zoo package for this,

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

answered Mar 31, 2017 at 14:23

Sotos

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1 Comment

G. Grothendieck Over a year ago

Note that this can also be written as: sapply(strsplit(df1$sequence, ''), rollapply, 7, paste, collapse = '')

akrun · Accepted Answer · 2017-03-31 14:29:52Z

We can modify the function to create a list to store the output that comes from each 'i'

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"

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