Lists are vectors, but as long as they aren't doing too much C++, or assert
specific types, it should work. Functions like length(), names(), [, etc
dispatch to both S3 and S4.
On Thu, Apr 23, 2015 at 6:11 PM, Ryan Thompson r...@thompsonclan.org wrote:
It looks like dplyr has support for base
Sure, but the way DataFrame is flexible is by relying on two abstractions
in base R. Just length() and '['. If dplyr does the same thing, which seems
totally reasonable, everything should work the same.
On Thu, Apr 23, 2015 at 4:32 PM, Vincent Carey st...@channing.harvard.edu
wrote:
Seems to me
Good catch. We'll want the strand in case we need to go back to a GRanges.
I would make the strand addition optional with the default of FALSE. It's
nice to have a column of strings you can paste right into a genome browser
(sorry Michael :-) ). I often pass my bench collaborators a spreadsheet
On 04/24/2015 11:08 AM, Peter Haverty wrote:
Good catch. We'll want the strand in case we need to go back to a GRanges.
I would make the strand addition optional with the default of FALSE.
It's nice to have a column of strings you can paste right into a genome
browser (sorry Michael :-) ). I
Going the other way can look like this:
##' Parse one or more location strings and return as a GRanges
##'
##' Parse one or more location strings and return as a GRanges. GRanges
will get the names from the location.strings.
##' @param location.string character
##' @export
##'
Those are all good reasons for keeping the strand by default. I'm on board.
Pete
Peter M. Haverty, Ph.D.
Genentech, Inc.
phave...@gene.com
On Fri, Apr 24, 2015 at 11:26 AM, Herv� Pag�s hpa...@fredhutch.org wrote:
On 04/24/2015 11:08 AM, Peter Haverty wrote:
Good catch.
Taking this a bit off topic but it would be nice if we could get the
GRanges equivalent of as.data.frame(table(x)), i.e., unique(x) with a count
mcol. Should be easy to support but what should the API be like?
On Fri, Apr 24, 2015 at 10:54 AM, Hervé Pagès hpa...@fredhutch.org wrote:
On
dplyr internally converts all `data.frame` objects to its `tbl_df` class
and most dplyr methods operate on the `tbl` superclass, see (
https://github.com/hadley/dplyr/blob/master/R/tbl-df.r,
https://github.com/hadley/dplyr/blob/master/R/tbl.r).
The most direct route would to getting DataFrame
On Fri, Apr 24, 2015 at 7:42 AM, Jim Hester james.f.hes...@gmail.com
wrote:
dplyr internally converts all `data.frame` objects to its `tbl_df` class
and most dplyr methods operate on the `tbl` superclass, see (
https://github.com/hadley/dplyr/blob/master/R/tbl-df.r,
Poster registration is now open. Visit the web site
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On 04/24/2015 09:07 AM, James W. MacDonald wrote:
A poster on the support site reported some warnings issued when running
hyperGTest() from GOstats. I tracked this down to the ls() function from
AnnotationDbi, when it dispatches on AnnDbBimap objects. The method is:
setMethod(ls,
Sorry, one more concern, if you're thinking of using as a range key, you
will need the strand, but many use cases might not want the strand on
there. Like for pasting into a genome browser.
On Fri, Apr 24, 2015 at 10:18 AM, Michael Lawrence micha...@gene.com
wrote:
It is a great idea, but I'm
It is a great idea, but I'm not sure I would use it to implement table().
Allocating those strings will be costly. Don't we already have the 4-way
int hash? Of course, my intuition might be completely off here.
On Fri, Apr 24, 2015 at 9:59 AM, Hervé Pagès hpa...@fredhutch.org wrote:
Hi Pete,
On 04/24/2015 10:18 AM, Michael Lawrence wrote:
It is a great idea, but I'm not sure I would use it to implement
table(). Allocating those strings will be costly. Don't we already have
the 4-way int hash? Of course, my intuition might be completely off here.
It does use the 4-way int hash
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