An anonymous student found this.
PREP
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
EXAMPLE
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
seqlevels(txdb, force=TRUE) <- c("chr22")
gr <- GRanges(seqnames = "chr22", ranges = IRanges(start = 1, end =
52330658))
gr.trans.chr22 <- su
On 09/21/2015 10:39 AM, Hervé Pagès wrote:
On 09/21/2015 02:06 AM, Christian Arnold wrote:
Hi Jim, Kasper, and Hervé,
thanks a lot for the quick answer. For some reason, I was under the
impression that I have to use exactly the original prototype from the
generics, but I didn't fully realize
On 09/21/2015 02:06 AM, Christian Arnold wrote:
Hi Jim, Kasper, and Hervé,
thanks a lot for the quick answer. For some reason, I was under the
impression that I have to use exactly the original prototype from the
generics, but I didn't fully realize I can extend this arbitrarily as
long as the o
This situation is complicated due to deficiencies in git-svn. The safest
(and most limiting) thing to do is to
git clone https://github.com/sneumann/mtbls2/
update_remotes.sh
git checkout devel
Then restrict all further development to the `devel` branch, sync it with
SVN via `git svn
Hi Robert,
On Sa, 2015-09-19 at 01:14 +, Robert M. Flight wrote:
> I think the simplest course is to leave your remote as is, and not use
> the Bioconductor mirror as a true remote.
Great, I like this approach.
> Instead, keep using the git-svn bridge to push to Bioconductor. And
> put you
Hi Christian,
This has not much to do with roxygen. 'R CMD check' complains that your
"counts" method doesn't have the arguments that your man page says it
has. Your method is defined with arguments (object, ...) but the \usage
section in the man page says it has arguments (object, type, readGrou
Hi Jim, Kasper, and Hervé,
thanks a lot for the quick answer. For some reason, I was under the
impression that I have to use exactly the original prototype from the
generics, but I didn't fully realize I can extend this arbitrarily as
long as the original arguments - object and ... in this case
It sounds like everything is working, apart from roxygen 2. This is the
right way to do this; there are many examples; for example findOverlaps for
GenomicRanges, GenomicRanges which support ignore.strand which is not an
argument to the generic; see below. You may have to discuss this with the
ro
Christian,
You need to use your extended prototype in the function definition within
your `setMethod()` call. In particular you do _not_ need to write an
explicit `@usage` directive.
See https://github.com/jimhester/examplePrototype/blob/master/R/package.R
for an example package without any NOTE
