storing long strings (DNA sequence) in R

Question

I have written a function that finds the indices of subsequences in a long DNA sequence. It works when my longer DNA sequence is < about 4000 characters. However, when I

Answer 1

Rather than write your own function, why not use the function words.pos in package seqinr. It seems to work even for strings up to a million base pairs.

For example,

library(seqinr)
data(ec999)
myseq <- paste(ec999[[1]], collapse="")
myseq <- paste(rep(myseq,100), collapse="")
words.pos("atat", myseq)

Answer 2

I can replicate nrussell's example, but this assigns correctly x<-paste0(rep("abcdef",1000),collapse="") -- a potential workaround is writing the character string to a .txt file and reading the .txt file into R directly:

test.txt is a 6,000 character long string.

`test<-read.table('test.txt',stringsAsFactors = FALSE)
 length(class(test[1,1]))
[1] 1
class(test[1,1])
[1] "character"
 nchar(test[1,1])
[1] 6000`