Hi,

I have a data.frame of exons per each transcript and another, corresponding, data.frame of the cds intervals:

exon.df <- data.frame(id=c(rep("id1",4),rep("id2",3),rep("id3",5)),
                      start=c(10,20,30,40,100,200,300,1000,2000,3000,4000,5000),
                      end=c(15,25,35,45,150,250,350,1500,2500,3500,4500,5500))


cds.df <- data.frame(id=c(rep("id1",3),rep("id2",3),rep("id3",3)),
                      start=c(20,30,40,125,200,300,2250,3000,4000),
                      end=c(25,35,45,150,250,325,2500,3500,4250))

I would like to extract the UTRs from these data for each transcript. For this example, the outcomes will be:

utr5.df <- data.frame(id=c("id1","id2","id3","id3"),
                     start=c(10,100,1000,2000),
                     end=c(15,124,1500,2249))

utr3.df <- data.frame(id=c("id2","id3","id3"),
                     start=c(326,4251,5000),
                     end=c(350,4500,5500))

Can GenomicRanges or any other package be used in any way for that?

One way would be to add a dummy "chr" variable and call GRanges() on both your exon.df and cdf.df to get GRanges objects. Then, split() them by "id" into GRangesList objects. Call range() on the exons to get the transcript bounds, then subtract the CDS regions from those to get the UTRs.

Something like (untested):

exon.df$chr <- "foo"
cds.df$chr <- "foo"
exon.gr <- GRanges(exon.df)
cds.gr <- GRanges(cds.df)
exon.grl <- split(exon.gr, ~ id)
cds.grl <- split(cds.gr, ~ id)
utr.grl <- psetdiff(unlist(range(exon.grl)), cds.grl)
stack(utr.grl, "id")