Hello,
Using Sweave to compile a long report, I get
tx19 <- loadDb("transcriptsHs19.db")
Error in loadDb(file, dbType, dbPackage, ...) :
error in evaluating the argument 'dbType' in selecting a method for function
'loadDb': Error: argument "dbType" is missing, with no default
The documenta
Michael,
According to my timings, here is where c() spends its time on GRanges
objects with 1 meta col:
- merging the seqinfo: 1.5%
- combining the seqnames: 5.9%
- combining the ranges: 12.4%
- combining the strand: 2%
- rbinding the mcols: 78.2%
It seems that any additional meta col
That GRanges only had one column, so I'm hoping that's not a lot of
overhead. The merging of the thousands of Seqinfo objects is probably the
issue. Any way to make that n-ary instead of a Reduce() over a binary merge?
Michael
On Tue, Jan 8, 2013 at 10:44 AM, Hervé Pagès wrote:
> Hi Dario,
>
>
Hi Martin,
On 8 Jan 2013, at 19:53, Martin Morgan wrote:
> On 01/07/2013 12:32 PM, Nicolas Delhomme wrote:
>> Hi Martin, Marc,
>>
>> I'm now implementing the use of BamFile objects in easyRNASeq and I like
>> them. I think it would be very useful if when constructing a BamFile the
>> existence o
On 01/07/2013 12:32 PM, Nicolas Delhomme wrote:
Hi Martin, Marc,
I'm now implementing the use of BamFile objects in easyRNASeq and I like
them. I think it would be very useful if when constructing a BamFile the
existence of the path and index could be tested; i.e. this works:
BamFile("test.bam",
Hi Dario,
On 01/06/2013 07:00 PM, Dario Strbenac wrote:
Are you asking if you can rewrite your code to work faster, or are you asking
if the BioC devs need to improve the code to be faster?
I was suggesting that maybe the c function for GRanges could be optimised.
Another would be manually
