It's difficult in general to have a coercion method from a less structured
data type (like a data frame) to one more structured/constrained (like a
GRanges). There's just no conventions as to how data is stored in the data
frame. The RangedData coercion is not biology-aware, so it is not going to
interact well with something output from GenomicRanges. I would recommend
the approach you took. It can be made a little cleaner via with().

I've been messing around with an import.trackTable in rtracklayer. It
allows the client to specify the positions of the seqnames, start and end
in a table. Currently it is internal though, in support of import of
generic tabix data.

Michael

On Sat, Nov 26, 2011 at 1:40 PM, Fahim Mohammad <fahim.md@gmail.com> wrote:

> Brute force method to do the same.
>
> load('/home/fahim/rugit/rangeData/hg19/GeneName.RData')
> head(data)
> fldslen = length(names(data)) #how many fields
> gr = GRanges(seqnames = Rle(data$seqnames), IRanges(data$start, data$end),
>  strand = Rle(as.character(data$strand)), name = data$name )
> if (fldslen > 6)
> {
>  restfldnames = setdiff(names(data), c('seqnames', 'start', 'end',
> 'strand', 'width', 'name'))
>  elementMetadata(gr) = datarest
> }
>
>
>
> 2011/11/26 Fahim Mohammad <fahim.md@gmail.com>
>
> > Hi
> >
> > I generated a data frame from GRanges object by performing
> >
> > data = as.data.frame (grObj, row.names =NULL);  #grObject is GRanges
> > object having 'seqnames' as one of its field.
> > save (data, file = ..)
> >
> > Now I want to read this data file again as GRanges object.
> >
> > Is there any built-in method to do that?  ( 'as' method in GRanges is
> > currently is not able to do it.)
> >
> > Alternatively, I tried to convert the data frame into RangedData first
> and
> > then into GRanges. But the conversion into RangedData assumed the
> > 'seqnames' as metadata and by default inserted 'space' with value '1' in
> >  IRanges. This conversion cast a problem for GRanges coersion as
> 'seqnames'
> > are now in the metadata field which is reserved keyword and thus
> producing
> > error.
> >
> >
> > > library(IRanges)> library(GenomicRanges)>
> load('/home/fahim/hg19/GeneName.RData')> head(data)  seqnames start   end
> width strand         name
> > 1     Chr1 10954 11507   554      + LOC100506145
> > 2     Chr1 12190 13639  1450      + LOC100652771
> > 3     Chr1 14362 29370 15009      -       WASH7P
> > 4     Chr1 30366 30503   138      +    MIR1302-2
> > 5     Chr1 34611 36081  1471      -      FAM138A
> > 6     Chr1 52453 53396   944      +       OR4G4P> rd1 = as(data,
> "RangedData")> rd1RangedData with 36590 rows and 3 value columns across 1
> space
> >          space               ranges   | seqnames   strand         name
> >       <factor>            <IRanges>   | <factor> <factor>     <factor>
> > 1            1     [ 10954,  11507]   |     Chr1        + LOC100506145
> > 2            1     [ 12190,  13639]   |     Chr1        + LOC100652771
> > 3            1     [ 14362,  29370]   |     Chr1        -       WASH7P
> > 4            1     [ 30366,  30503]   |     Chr1        +    MIR1302-2
> > 5            1     [ 34611,  36081]   |     Chr1        -      FAM138A
> > 6            1     [ 52453,  53396]   |     Chr1        +       OR4G4P
> > 7            1     [ 63016,  63885]   |     Chr1        +      OR4G11P
> > 8            1     [ 69091,  70008]   |     Chr1        +        OR4F5
> > 9            1     [131125, 135677]   |     Chr1        + LOC100420257
> > ...        ...                  ... ...      ...      ...          ...
> > 36582        1 [59100457, 59115123]   |     ChrY        +        SPRY3
> > 36583        1 [59160762, 59162330]   |     ChrY        -        AMDP1
> > 36584        1 [59213949, 59276439]   |     ChrY        +        VAMP7
> > 36585        1 [59311663, 59311996]   |     ChrY        -     TCEB1P24
> > 36586        1 [59318017, 59318918]   |     ChrY        -       TRPC6P
> > 36587        1 [59330252, 59343488]   |     ChrY        +         IL9R
> > 36588        1 [59354329, 59358343]   |     ChrY        +       WASH6P
> > 36589        1 [59358332, 59360854]   |     ChrY        -     DDX11L16
> > 36590        1 [59361222, 59361778]   |     ChrY        - LOC100507426>
> rd2 = as(rd1, "GRanges")Error in validObject(.Object) :
> >   invalid class "GRanges" object: slot 'elementMetadata' cannot use
> "seqnames", "ranges", "strand", "seqlevels", "seqlengths", "isCircular",
> "genome", "start", "end", "width", "element" as column names
> >
> >  >
> >
>
>
>
> --
>
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>
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