Generating all gapped k-mer sequences from string - r

Question

I am interested in making all gapped-kmers from a sequence, with gapped-kmer defined as a sequence of length k separated by up to m positions from another sequence of length k. So for example, "sequence CAGAT the gappy pair
kernel with k = 1 and m = 2 finds pairs of monomers with zero to two irrelevant positions in between. i.e. it finds the features CA, C.G, C..A, AG, A.A, A..T, GA, G.T and AT"
replacefxn <- function(x, k, m) {
substr(x, k + 1, k + m) <- paste(rep("X", m), collapse = "")
return(x)
}
gappedkmersfxn <- function(x, k, m) {
n <- (2 * k + m)
subseq <-
substring(x, seq(from = 1, to = (nchar(x) - n + 1)), seq(from = n, to = nchar(x)))
return(sapply(subseq, replacefxn, k, m))
}
allgappedkmersfxn <- function(x, k, m) {
kmers <- list()
for (i in 0:m) {
kmers[[i]] <- gappedkmersfxn(x, k, i)
}
kmers <- unlist(kmers)
return(kmers)
}
allgappedkmersfxn is how I have it implemented currently, but it does not add the features with no gap (m is maximum gap, but goes from 0 to m), thus not giving me all of the desired features (see example of "CAGAT"). In addition, it is very slow and inefficient when doing millions of sequences at a time. It is also coded poorly, but with limited experience in R I am not sure how to improve it.
What would the most efficient way of doing this be while making sure that all expected subsequences (ex: CAGAT -> CA, C.G, C..A, AG, A.A, A..T, GA, G.T and AT for k=1, m=2) are included in the output?
Thanks!

Answer 1

You may want to look at the implementation of a gappy pair kernel in the Bioconductor kebabs package.
Installation:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("kebabs")
To generate a k = 1, m = 2 kernel:
library(kebabs)
gappyK1M2 <- gappyPairKernel(k = 1, m = 2)
To generate an explicit representation from a DNA sequence:
dnaseqs <- DNAStringSet("CAGAT")
dnaseqsrep <- getExRep(dnaseqs, gappyK1M2)
The k-mers are stored in the Dimnames slot:
dnaseqsrep#Dimnames[[2]]
[1] "A.A" "AG" "AT" "A..T" "CA" "C..A" "C.G" "GA" "G.T"