On 03/31/2016 07:05 AM, Michael Lawrence wrote:
We should probably deprecate values(). It has long been superseded by
mcols().
FWIW this is on my long-term list but it can't be done now. values()
was originally (and is still) a RangedData accessor. At some point it
was also made a synonym of elementMetadata() (a.k.a. mcols()) for
Vector derivatives. The goal was to make it easier for package
developers to write code that would operate the same way on GRanges
or RangedData objects. I think easyRNASeq is one of those packages.
Those packages need to be modified to use only GRanges objects
before they can start using mcols() instead of values(). It will
take a long time before we can deprecate values()...
H.
But for now, it would seem pragmatic to importFrom(hash, ...)
since it has so few functions.
On Thu, Mar 31, 2016 at 6:54 AM, Zhu, Lihua (Julie)
<julie....@umassmed.edu> wrote:
Sorry. I meant values.
replacing previous import ŒIRanges::values¹ by Œhash::values¹ when loading
ŒCRISPRseek¹
Best,
Julie
On 3/30/16 11:13 PM, "Michael Lawrence" <lawrence.mich...@gene.com> wrote:
I can't find the hash function in IRanges. Are you sure it has one?
On Wed, Mar 30, 2016 at 8:07 PM, Zhu, Lihua (Julie)
<julie....@umassmed.edu> wrote:
Michael,
I have the same user case as Kasper. Another example is that both
IRanges
and hash packages have hash. I need to use the hash from the hash
package
instead of the one from IRanges.
Best,
Julie
On Mar 30, 2016, at 7:57 PM, Kasper Daniel Hansen
<kasperdanielhan...@gmail.com> wrote:
My usecase is when I import() two packages who has a conflict in a name.
For example, both Biobase and matrixStats has both anyMissing and
rowMedians. I am happy to get all of these two packages, but I need to
resolve the conflict. Since I want to keep the ones from matrixStats I
know
need to figure out how to import Biobase selectively. Which I can,
using
the tools from codetoolsBioC, but I would also be happy with an
importFromExcept(), which would make my life much easier.
Best,
Kasper
On Wed, Mar 30, 2016 at 4:47 PM, Michael Lawrence
<lawrence.mich...@gene.com> wrote:
I'm curious about which symbols you wouldn't want to import, and why.
On Wed, Mar 30, 2016 at 12:19 PM, Zhu, Lihua (Julie)
<julie....@umassmed.edu> wrote:
Hi,
Is there a function to import all the exported objects from a package
except a few named ones in NAMESPACE file?
For example, I would like to import all the functions in S4Vectors
except fold. Is there a way to specify this without listing all
other
functions using importFrom?
Many thanks for your help!
Best regards,
Julie
********************************************
Lihua Julie Zhu, Ph.D
Research Professor
Department of Molecular, Cell and Cancer Biology (MCCB)
Head of MCCB Bioinformatics Core
Program in Molecular Medicine
Program in Bioinformatics and Integrative Biology
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
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