Multiple unions

Question

I am trying to do unions on several lists (these are actually GRanges objects not integer lists but the priciple is the same), basically one big union.

x<         


        

Answer 1

A not necessarily memory efficient paradigm that will work with GRanges is

Reduce(union, list(x, y, z))

The argument might also be a GRangesList(x, y, z) for appropriate values of x etc.

Answer 2

unique(unlist(mget(mylists, globalenv())))

will do the trick. (Possibly changing the environment given in the call to mget, as required.)

Answer 3

ok this works but I am curious why sapply seems to have its own scope

x<-sort(sample(1:20, 9))
y<-sort(sample(10:30, 9))
z<-sort(sample(20:40, 9))
mylists<-c("x","y","z")
emptyList<-vector()
for(f in mylists){emptyList<-union(emptyList,get(f))}

Answer 4

I think it would be cleaner to separate the "dereference" part from the n-ary union part, e.g.

dereflist <- function(l) lapply(a,get)
nunion <- function(l) Reduce(union,l)

But if you look at how union works, you'll see that you could also do

nunion <- function(l) unique(do.call(c,l))

which is faster in all the cases I've tested (much faster for long lists).

-s

Answer 5

x<-sort(sample(1:20, 9))
y<-sort(sample(10:30, 9))
z<-sort(sample(20:40, 9))

Both of the below produce the same output

unique(c(x,y,z))
[1]  1  2  4  6  7  8 11 15 17 14 16 18 21 23 26 28 29 20 22 25 31 32 35

union(x,union(y,z))
[1]  1  2  4  6  7  8 11 15 17 14 16 18 21 23 26 28 29 20 22 25 31 32 35