Dear Bioconductors,
The Department of Biostatistics at the University of Washington, Seattle
has a position open for a Research Scientist/Engineer 4. Basic
responsibilities are to provide data analysis, programming, experimental
design, interpretation and reporting of results for statistical
Thanks Martin,
I am using \thanks now. It works.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 12/19/13 5:53 PM, "Martin Morgan" wrote:
>On 12/19/2013 01:44 PM, Ou, Jianhong wrote:
>> Hi All,
>>
>> I tried to add
Thanks Herve, Robert,
Now it works good.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 12/20/13 2:25 PM, "Hervé Pagès" wrote:
>Hi Robert, Jianhong,
>
>This could be related to some changes to the relist() and sp
Hi Leonard,
What happened between GenomicAlignments 0.99.8 and
GenomicAlignments 0.99.10 is that I modified
readGAlignmentPairsFromBam() to use the new pairing algo
(implemented in scanBam()) instead of the pairing algo
implemented by findMateAlignment():
Hi Robert, Jianhong,
This could be related to some changes to the relist() and split() code
that I made a few days ago in IRanges. I didn't immediately make the
corresponding changes to GenomicRanges and GenomicAlignments so
relisting or splitting GRanges and GAlignments objects was broken for
a
hi,
i can reproduce what Jianhong says, i noticed it earlier this week but
didn't mention because we all know devel is a moving target and so on,
but since this has been raised now i'll report what i'm getting.
so, this is for Jianhong, if you downgrade the following packages to
these partic
In my case, looks like never end.
I need to check my R first.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 12/20/13 12:05 PM, "Hervé Pagès" wrote:
>Hi Jianhong,
>
>According to my timings, it's a little bit slow
Hi Jianhong,
According to my timings, it's a little bit slower than exonsBy() but
not that much. It has to do a little bit more work too as the introns
are not explicitly stored in the SQLite db (the exons are) but are
inferred from the exons and transcript boundaries.
So intronsByTranscript() ha
Depends on what you mean by unacceptably slow. Took me almost 20
seconds, during which time I got pretty fidgety.
> system.time(introns <-
intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene))
user system elapsed
18.741 0.204 19.340
How long did it take you, and how much RAM do you
Dear all,
When I try to use intronsByTranscript to get introns for hg19 known genes, I
found it is unacceptable slow. Does any body has the same problem?
My code:
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
introns <- intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene)
Thanks Steven. Very clear.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 12/19/13 5:54 PM, "Steven McKinney" wrote:
>Yes, floating point issue.
>
>See e.g.
>
>http://cran.r-project.org/doc/FAQ/R-FAQ.html
>7.31 Wh
Hi Michael,
On 11/12/2013 11:31 AM, Hervé Pagès wrote:
Hi Michael,
On 11/12/2013 10:27 AM, Michael Lawrence wrote:
Seems like the output could be more consistent with the behavior on
DNAStringSet, i.e., the counts could be named.
alphabetFrequency(AAString("CYGGAGTRQ"))
[1] 0 0 0 0 0 0 0
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