R - fail to store multiple output from for loop in vector or data frame

Question

I have a data frame called lbt_all_epitopes of 38282 rows and three columns, as shown below:

 sequence    score epitope.
1 RPGGPPGYRTPYTAK 1.724911  Epitope
2 TQGDRQKIQDAVSAA 1.664611  Epitope
3 EVKSRYNVDVSQNKR 1.593236  Epitope
4 VIEMTRAFEDDDFDK 1.578200  Epitope
5 ITQGDRQKIQDAVSA 1.533208  Epitope
6 GSADLTPSNLTRPAS 1.532700  Epitope

In the first column (named sequence) I have multiple similar strings, which I want to remove (I will be looking for similar strings using str_sub). For example, considering the first string of lbt_all_epitopes$sequence ("RPGGPPGYRTPYTAK") I want to look for similar strings in the whole column and store them in a vector or in a data.frame, which will be called to_be_removed. I want to do this iteration for the first 30 elements present in lbt_all_epitopes$sequence. For the sake of simplicity, let's just consider the top five rows. When I run the loop, like the one below:

# Iterate over the first 5 rows
top_30 <- 1:5

for(i in top_30) {
  print(agrep(str_sub(lbt_all_epitopes$sequence[i], start = 5, end = 11), lbt_all_epitopes$sequence, value = T))
}

The output:

 [1] "RPGGPPGYRTPYTAK" "VGTRPGGPPGYRTPY" "TRPGGPPGYRTPYTA" "GGPPGYRTPYTAKPF" "PGGPPGYRTPYTAKP"
 [6] "LVGTRPGGPPGYRTP" "TLVGTRPGGPPGYRT" "GPPGYRTPYTAKPFV" "PPGYRTPYTAKPFVM" "GTRPGGPPGYRTPYT"
[11] "PGYRTPYTAKPFVMC"
 [1] "TQGDRQKIQDAVSAA" "ITQGDRQKIQDAVSA" "GITQGDRQKIQDAVS" "NGITQGDRQKIQDAV" "QGDRQKIQDAVSAAS"
 [6] "QNGITQGDRQKIQDA" "GDRQKIQDAVSAASS" "VQNGITQGDRQKIQD" "DRQKIQDAVSAASSW" "RQKIQDAVSAASSWL"
[11] "QKIQDAVSAASSWLE"
 [1] "EVKSRYNVDVSQNKR" "VKSRYNVDVSQNKRA" "NEVKSRYNVDVSQNK" "KSRYNVDVSQNKRAR" "LNEVKSRYNVDVSQN"
 [6] "YNVDVSQNKRARLRL" "RYNVDVSQNKRARLR" "MLNEVKSRYNVDVSQ" "SRYNVDVSQNKRARL" "HMLNEVKSRYNVDVS"
[11] "EHMLNEVKSRYNVDV"
 [1] "VIEMTRAFEDDDFDK" "RVIEMTRAFEDDDFD" "GDRVIEMTRAFEDDD" "DRVIEMTRAFEDDDF" "IEMTRAFEDDDFDKF"
 [6] "RGDRVIEMTRAFEDD" "EMTRAFEDDDFDKFD" "FRGDRVIEMTRAFED" "MTRAFEDDDFDKFDR" "TRAFEDDDFDKFDRV"
[11] "RAFEDDDFDKFDRVR"
 [1] "TQGDRQKIQDAVSAA" "ITQGDRQKIQDAVSA" "GITQGDRQKIQDAVS" "NGITQGDRQKIQDAV" "QGDRQKIQDAVSAAS"
 [6] "QNGITQGDRQKIQDA" "GDRQKIQDAVSAASS" "VQNGITQGDRQKIQD" "DVQNGITQGDRQKIQ" "DRQKIQDAVSAASSW"
[11] "RQKIQDAVSAASSWL"

Is exactly what I want i.e. it printed all the similar strings (11 per iteration) to the first, second, third...fifth elements of lbt_all_epitopes$sequence. However, when I try to store the output in a vector (called to_be_removed), with the following loop:

# create the empty vector where I will store the output
to_be_removed <- c()

for(i in top_30) {
  to_be_removed[i] <- agrep(str_sub(lbt_all_epitopes$sequence[i], start = 5, end = 11), lbt_all_epitopes$sequence, value = T)
}

I noticed that each iteration produced only a single string as output (as opposed to 11 strings for each iteration), as below:

> to_be_removed
[1] "RPGGPPGYRTPYTAK" "TQGDRQKIQDAVSAA" "EVKSRYNVDVSQNKR" "VIEMTRAFEDDDFDK" "TQGDRQKIQDAVSAA"

The following warning message was displayed:

Warning messages:
1: In to_be_removed[i] <- agrep(str_sub(lbt_all_epitopes$sequence[i],  :
  number of items to replace is not a multiple of replacement length
2: In to_be_removed[i] <- agrep(str_sub(lbt_all_epitopes$sequence[i],  :
  number of items to replace is not a multiple of replacement length
3: In to_be_removed[i] <- agrep(str_sub(lbt_all_epitopes$sequence[i],  :
  number of items to replace is not a multiple of replacement length
4: In to_be_removed[i] <- agrep(str_sub(lbt_all_epitopes$sequence[i],  :
  number of items to replace is not a multiple of replacement length
5: In to_be_removed[i] <- agrep(str_sub(lbt_all_epitopes$sequence[i],  :
  number of items to replace is not a multiple of replacement length

I am then assuming that I am missing the code telling R that it should also concatenate all the strings produced by each iteration, then go to the next iteration. Does anyone know how to correctly store the output in a vector, or even in a data.frame?

Answer 1

You can create a list :

# create the empty vector where I will store the output
to_be_removed <- list()

for(i in top_30) {
  to_be_removed[[i]] <- agrep(str_sub(lbt_all_epitopes$sequence[i], start = 5, end = 11), lbt_all_epitopes$sequence, value = T)
}

Notice the double bracket to fill the list.

Also next time please post your data using dput so we can use it directly. To do so do : dput(lbt_all_epitopes) which returns :

structure(list(X = 1:6, sequence = structure(c(4L, 5L, 1L, 6L, 
3L, 2L), .Label = c("EVKSRYNVDVSQNKR", "GSADLTPSNLTRPAS", "ITQGDRQKIQDAVSA", 
"RPGGPPGYRTPYTAK", "TQGDRQKIQDAVSAA", "VIEMTRAFEDDDFDK"), class = "factor"), 
    score = structure(c(6L, 5L, 4L, 3L, 2L, 1L), .Label = c("1.532700", 
    "1.533208", "1.578200", "1.593236", "1.664611", "1.724911"
    ), class = "factor"), epitope. = structure(c(1L, 1L, 1L, 
    1L, 1L, 1L), .Label = "Epitope", class = "factor")), .Names = c("X", 
"sequence", "score", "epitope."), class = "data.frame", row.names = c(NA, 
-6L))

Answer 2

To avoid a growing for()-loop, we can use lapply(). This should be faster when handling huge datasets.

to_be_removed <- lapply(lbt_all_epitopes$sequence[1:5], function(x) agrep(str_sub(x, start = 5, end = 11), lbt_all_epitopes$sequence, value = T))

gives a list with the extracted strings for each row in a separate list entry:

[[1]]
[1] "RPGGPPGYRTPYTAK"

[[2]]
[1] "TQGDRQKIQDAVSAA" "ITQGDRQKIQDAVSA"

[[3]]
[1] "EVKSRYNVDVSQNKR"

[[4]]
[1] "VIEMTRAFEDDDFDK"

[[5]]
[1] "TQGDRQKIQDAVSAA" "ITQGDRQKIQDAVSA"

Now you can separate those with strsplit() and unlist() them into a vector (which you could use to subset):

to_be_removed <- unlist(lapply(to_be_removed, function(x) strsplit(x, " ")))

Output:

[1] "RPGGPPGYRTPYTAK" "TQGDRQKIQDAVSAA" "ITQGDRQKIQDAVSA" "EVKSRYNVDVSQNKR" "VIEMTRAFEDDDFDK" "TQGDRQKIQDAVSAA"
[7] "ITQGDRQKIQDAVSA"