ok here are a few options. The latter seems to be exactly what you want ...
x<-1:5
y<-1:5
z<-1:5
xy<-data.table(x,y,z)
NEWxy<-subset(xy, select = -c(x,y) ) #removes column x and y
and
id<-c("x","y")
newxy<-xy[, id, with=FALSE]
newxy #gives just x and y e.g.
# x y
#[1,] 1 1
#[2,] 2 2
#[3,] 3 3
#[4,] 4 4
#[5,] 5 5
and finally what you really want:
anotherxy<-xy[,id:=NULL,with=FALSE] # removes comuns x and y that are in id
# z
#[1,] 1
#[2,] 2
#[3,] 3
#[4,] 4
#[5,] 5
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