There is a lot of meat here that I can't properly address now because I
am heading out to serve as a BioC evangelist in Europe. I was looking
over the as.env methods that you created Michael and I agree it would be
useful if we expanded upon this to support Rle's. I probably wont be
able to do much work on this until late June, but Michael feel free to
rework this as you see fit.
Cheers,
Patrick
On 6/5/10 9:18 AM, Charles C. Berry wrote:
On Fri, 4 Jun 2010, Patrick Aboyoun wrote:
Great thread on the subset function. It currently has to
IRanges-based methods:
showMethods("subset")
Function: subset (package base)
x="ANY"
x="DataTable"
x="Sequence"
Based on what was being discussed, I see two enhancement requests:
1) Expanding the scope of subset to allow reference to components of
non-DataTable objects such as IRanges and GRanges instances:
## Currently not supported, but could be
ir <- IRanges(start = 1:10, end = 1:10)
subset(ir, start < 5)
2) Add support for subsetting by 'logical' Rle in the subset function.
The second request is straight-forward to implement since it can be
done within the subset methods of the Sequence and DataTable virtual
classes. If we limit the first to Ranges (virtual class) and GRanges
(which doesn't inherit from Ranges) objects, then two more subset
methods would suffice to achieve 1). Sound reasonable?
Patrick
Perhaps this request pertaining to xtabs(..., subset = ...) is related.
Currently (rather, in IRanges_1.6.4)
library(IRanges)
ir <-
RangedData(IRanges(start=1:10,width=1),space=rep(letters[1:2],5),z=rep(1:3,length=10))
xtabs(~z,as.data.frame(ir),subset = z > 1)
z
2 3
3 3
xtabs(~z,subset(ir,z>1))
z
2 3
3 3
xtabs(~z,ir,subset = z > 1)
Error in xj[i] : invalid subscript type 'closure'
xtabs(~z,subset(ir,space=='a'))
z
1 2 3
2 1 2
xtabs(~z,ir,subset = space=='a')
Error in xj[i] : invalid subscript type 'closure'
Can this be changed to allow use of the subset argument when the data
arg is a RangedData (or GRanges) instance?
Thanks,
Chuck
On 6/4/10 10:06 PM, Steve Lianoglou wrote:
Hi Vincent,
> the simplification that Steve
> seems to be asking for would
> allow implicit references to elementMetadata variables in the
predicate. > I
> am not in favor of such
> an extension of semantics of bracket.
>
Just to be clear, I'm not suggesting referencing elementMetadata
variables implicitly w/in brackets, but rather only when using
`subset` (as `subset` does now with columns of a data.frame (when it's
used *on* a data.frame))
So, using your example gr object:
GRanges with 10 ranges and 2 elementMetadata values
seqnames ranges strand | score GC
<Rle> <IRanges> <Rle> |<integer> <numeric>
a Chrom1 [ 1, 10] - | 1 1.0000000
b Chrom2 [ 2, 10] + | 2 0.8888889
c Chrom2 [ 3, 10] + | 3 0.7777778
d Chrom2 [ 4, 10] * | 4 0.6666667
e Chrom1 [ 5, 10] * | 5 0.5555556
f Chrom1 [ 6, 10] + | 6 0.4444444
g Chrom3 [ 7, 10] + | 7 0.3333333
h Chrom3 [ 8, 10] + | 8 0.2222222
i Chrom3 [ 9, 10] - | 9 0.1111111
j Chrom3 [10, 10] - | 10 0.0000000
seqlengths
Chrom1 Chrom2 Chrom3
NA NA NA
I was curious if this would be useful:
R> subset(gr, strand == "+"& score> 6)
but I wasn't trying to propose having something like this:
R> gr[strand == "+"& score> 6]
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Charles C. Berry (858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:[email protected] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
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