I have a GRanges object and I would like to get a list of GRange objects which are subsets of the original object, each of the the objects in this list should have the same position (same chr, start and end values).

library(GenomicRanges)
# input:
gr=GRanges(seqnames=c("chr1","chr1","chr2","chr2"),
           ranges=IRanges(start=c(50,50,200,200),end=c(100,100,300,300)),
           strand=c("+","+","-","-"),
           scores=c(0.5,0.5,0.5,0.5)
)
gr
>GRanges object with 4 ranges and 1 metadata column:
>      seqnames     ranges strand |    scores
>              | 
>  [1]     chr1 [ 50, 100]      + |       0.5
>  [2]     chr1 [ 50, 100]      + |       0.5
>  [3]     chr2 [200, 300]      - |       0.5
>  [4]     chr2 [200, 300]      - |       0.5
>  -------
>  seqinfo: 2 sequences from an unspecified genome; no seqlengths

# the desired output is an object of the form of ls
gr1=GRanges(seqnames=c("chr1","chr1"),
           ranges=IRanges(start=c(50,50),end=c(100,100)),
           strand=c("+","+")
)
gr1
>GRanges object with 2 ranges and 0 metadata columns:
>      seqnames    ranges strand
>            
>  [1]     chr1 [50, 100]      +
>  [2]     chr1 [50, 100]      +
>  -------
>  seqinfo: 1 sequence from an unspecified genome; no seqlengths

gr2=GRanges(seqnames=c("chr2","chr2"),
           ranges=IRanges(start=c(200,200),end=c(300,300)),
           strand=c("-","-"),
           scores=c(0.5,0.5)
)
gr2
>GRanges object with 2 ranges and 1 metadata column:
>      seqnames     ranges strand |    scores
>              | 
>  [1]     chr2 [200, 300]      - |       0.5
>  [2]     chr2 [200, 300]      - |       0.5
>  -------
>  seqinfo: 1 sequence from an unspecified genome; no seqlengths

ls <- list(gr1,gr2)
ls
>[[1]]
>GRanges object with 2 ranges and 0 metadata columns:
>      seqnames    ranges strand
>            
>  [1]     chr1 [50, 100]      +
>  [2]     chr1 [50, 100]      +
>  -------
>  seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
>[[2]]
>GRanges object with 2 ranges and 1 metadata column:
>      seqnames     ranges strand |    scores
>              | 
>  [1]     chr2 [200, 300]      - |       0.5
>  [2]     chr2 [200, 300]      - |       0.5
>  -------
>  seqinfo: 1 sequence from an unspecified genome; no seqlengths

For example in the excerpt from the GRanges object above the first 2 lines should be in a new GRanges object in a list of GRange objects and the last 2 lines in a second GRanges object in that list.

Any suggestions?

How about this:

split(gr, as.factor(gr))

>
GRangesList object of length 2:
$chr1:50-100:+ 
GRanges object with 2 ranges and 1 metadata column:
      seqnames    ranges strand |    scores
         <Rle> <IRanges>  <Rle> | <numeric>
  [1]     chr1 [50, 100]      + |       0.5
  [2]     chr1 [50, 100]      + |       0.5

$chr2:200-300:- 
GRanges object with 2 ranges and 1 metadata column:
      seqnames     ranges strand | scores
  [1]     chr2 [200, 300]      - |    0.5
  [2]     chr2 [200, 300]      - |    0.5

-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths

You can even do it without the as.factor() part and it seems to work, but I get a warning so maybe it's safer to use the first version.