I am sorry, but I still have a problem. With your syntax I get a vector
that is going over all chromosomes. How do I get , for instance separate
vectors for each chromosomes?
Thanks

2013/1/17 Hermann Norpois <hnorpois@googlemail.com>

> Hello,
>
> I would like to transform a GRange-object into something with density
> information related of bins, e.g. 1 bin=200bps. So it starts at poistion 1
> etc ...
> That means (according to testset.gr):
> bin 1    0
> bin 2    0
> ...
> bin 50  0
> bin 51    0.28        #10000-10200 => (200-144)/200
> bin 52    0.765        #10200-10400 => 153/200
> ...
> etc
> according to testset.gr (see below).
>
> How does it work? Is there a special function?
> Thanks
> Hermann
>
>
> > testset.gr
> GRanges with 20 ranges and 0 metadata columns:
>        seqnames           ranges strand
>           <Rle>        <IRanges>  <Rle>
>    [1]     chr1 [ 10144,  10353]      *
>    [2]     chr1 [ 10441,  10463]      *
>    [3]     chr1 [235633, 235766]      *
>    [4]     chr1 [237717, 237895]      *
>    [5]     chr1 [521444, 521624]      *
>    [6]     chr1 [540609, 540786]      *
>    [7]     chr1 [564495, 564672]      *
>    [8]     chr1 [565254, 566081]      *
>    [9]     chr1 [566537, 567272]      *
>    ...      ...              ...    ...
>   [12]     chr1 [569610, 570190]      *
>   [13]     chr1 [601057, 601196]      *
>   [14]     chr1 [713227, 713475]      *
>   [15]     chr1 [752533, 752578]      *
>   [16]     chr1 [752654, 752695]      *
>   [17]     chr1 [754405, 754539]      *
>   [18]     chr1 [755336, 755918]      *
>   [19]     chr1 [756027, 756458]      *
>   [20]     chr1 [756793, 756843]      *
>   ---
>   seqlengths:
>     chr1 chr10 chr11 chr12 chr13 chr14 ...  chr6  chr7  chr8  chr9  chrX
> chrY
>       NA    NA    NA    NA    NA    NA ...    NA    NA    NA    NA
> NA    NA
> > dput (testset.gr)
> new("GRanges"
>     , seqnames = new("Rle"
>     , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12",
> "chr13",
> "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2",
> "chr20", "chr21", "chr22", "chr3", "chr4", "chr5", "chr6", "chr7",
> "chr8", "chr9", "chrX", "chrY"), class = "factor")
>     , lengths = 20L
>     , elementMetadata = NULL
>     , metadata = list()
> )
>     , ranges = new("IRanges"
>     , start = c(10144L, 10441L, 235633L, 237717L, 521444L, 540609L,
> 564495L,
> 565254L, 566537L, 567450L, 568038L, 569610L, 601057L, 713227L,
> 752533L, 752654L, 754405L, 755336L, 756027L, 756793L)
>     , width = c(210L, 23L, 134L, 179L, 181L, 178L, 178L, 828L, 736L, 453L,
> 545L, 581L, 140L, 249L, 46L, 42L, 135L, 583L, 432L, 51L)
>     , NAMES = NULL
>     , elementType = "integer"
>     , elementMetadata = NULL
>     , metadata = list()
> )
>     , strand = new("Rle"
>     , values = structure(3L, .Label = c("+", "-", "*"), class = "factor")
>     , lengths = 20L
>     , elementMetadata = NULL
>     , metadata = list()
> )
>     , elementMetadata = new("DataFrame"
>     , rownames = NULL
>     , nrows = 20L
>     , listData = structure(list(), .Names = character(0))
>     , elementType = "ANY"
>     , elementMetadata = NULL
>     , metadata = list()
> )
>     , seqinfo = new("Seqinfo"
>     , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14",
> "chr15",
> "chr16", "chr17", "chr18", "chr19", "chr2", "chr20", "chr21",
> "chr22", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
> "chrX", "chrY")
>     , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_,
> NA_integer_,
> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
> NA_integer_, NA_integer_, NA_integer_, NA_integer_)
>     , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
> NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA)
>     , genome = c(NA_character_, NA_character_, NA_character_,
> NA_character_,
> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_
> )
> )
>     , metadata = list()
> )
> >
>

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