Hi Martin
On 09/06/15 15:35, Martin Morgan wrote:
In case you missed it in Marc's reply, and acknowledging that this is
different from your suggestion, there is mapIds() for doing this on a
single column basis, which is the common use case where one doesn't care
too much about multiple mapping
hi,
currently, the annotation of variants in intronic regions by
VariantAnnotation and the locateVariants() function does not assign
strand to annotations in introns:
library(VariantAnnotation)
example(locateVariants)
loc_all[loc_all$LOCATION == "intron"]
GRanges object with 2 ranges and 9 me
As select() works currently, the returned keys are in identical order as
the input, with extra rows inserted as needed. And any one-to-nothing
mapping results in a NA returned. So by definition my (admittedly naive)
method is guaranteed to work. But your point is well taken - match() is
safer. But
On 06/08/2015 11:43 PM, Rainer Johannes wrote:
dear Robert and Ludwig,
the EnsDb packages provide all the gene/transcript etc annotations for all
genes defined in the Ensembl database (for a given species and Ensembl
release). Except the column/attribute "entrezid" that is stored in the
internal
On 06/09/2015 02:52 AM, Simon Anders wrote:
Hi
My two cents:
On 04/06/15 19:50, James W. MacDonald wrote:
In other words, for me it is a common practice to do something like this:
fit <- lmFit(eset, design)
fit2 <- eBayes(fit)
gns <- select(, featureNames(eset), c("ENTREZID","SYMBOL"))
gns <-
See https://bioconductor.org/BioC2015/ for details.
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Hi
My two cents:
On 04/06/15 19:50, James W. MacDonald wrote:
In other words, for me it is a common practice to do something like this:
fit <- lmFit(eset, design)
fit2 <- eBayes(fit)
gns <- select(, featureNames(eset), c("ENTREZID","SYMBOL"))
gns <- gns[!duplicated(gns[,1]),]
fit2$genes <- gns
dear Ludwig,
On 09 Jun 2015, at 10:46, Ludwig Geistlinger
mailto:ludwig.geistlin...@bio.ifi.lmu.de>>
wrote:
Dear Johannes,
Thx for providing the great EnsDb packages!
One question:
As of now, I am able to choose between TxDb and EnsDb for genomic
coordinates of genomic features such as genes
Dear Johannes,
Thx for providing the great EnsDb packages!
One question:
As of now, I am able to choose between TxDb and EnsDb for genomic
coordinates of genomic features such as genes, transcripts, and exons.
For the sequences themselves I need the corresponding BSgenome package.
While it is e
