How to get the recombined vectors efficiently? - r

Question

Given two axises, both with positions from 1 to N (N can be several millions, but we assume N = 1000 here),
there are two vectors recording the positions of some points on the two axises, respectively. For example:
chrm1 <- c(1, 35, 456, 732) # 4 points on axis 1 at position 1, 35, 456, 732;
chrm2 <- c(23, 501, 980)
if recombination at position 300 of the two axis, points behind 300 on the two axises will switch to the other axis.
the two vectors recording position of points will become :
chrm1 <- c(1, 35, 501, 980)
chrm2 <- c(23, 456, 732)
if a second recombination occurs at 600, the new vectors will be:
chrm1 <- c(1, 35, 501, 732)
chrm2 <- c(23, 456, 980)
the real data looks like this:
set.seed(1)
chrm1 <- sample.int(1e8, 50)
chrm2 <- sample.int(1e8, 50)
breaks.site <- sample.int(1e8, 5)
My brute-force way was to swap points into the other vector for each breaks sites. But this is quite slow, because I have to do this for 2 x 1000 x 20000 times.
How to get the recombined vectors efficiently?
for(i in breaks.site){
chrm1.new <- c(chrm1[chrm1 < i], chrm2[chrm2 > i])
chrm2.new <- c(chrm1[chrm1 > i], chrm2[chrm2 < i])
chrm1 <- chrm1.new
chrm2 <- chrm2.new
}
background about recombination:
https://en.wikipedia.org/wiki/Genetic_recombination

Answer 1

Maybe this:
chrm1 <- c(1, 35, 456, 732)
chrm2 <- c(23, 501, 980)
breaks <- c(300, 600)
#check all points for all breaks,
#get sum of position changes and
#calculate x mod 2
changepos1 <- rowSums(outer(chrm1, breaks, ">")) %% 2
changepos2 <- rowSums(outer(chrm2, breaks, ">")) %% 2
#assemble results and sort
res1 <- sort(c(chrm1[!changepos1], chrm2[as.logical(changepos2)]))
#[1] 1 35 501 732
res2 <- sort(c(chrm2[!changepos2], chrm1[as.logical(changepos1)]))
#[1] 23 456 980
If outer needs to much memory due to the size of your problem, you can use a loop instead.