User: Michael Lawrence

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Posts by Michael Lawrence

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Answer: A: rtracklayer issue (getTable)
... On Mon, Oct 5, 2009 at 9:55 AM, Marc Carlson wrote: > Whoa. > > Do you still plan to have the default behavoir be just chromosome X? > Because that would be quite surprising to me... > > Thinking about this some more, this would be surprising to those just wanting to use rtrackla ...
written 10.2 years ago by Michael Lawrence620
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Comment: C: rtracklayer issue (getTable)
... Hi Mark, I was not planning on porting the fix to the released version, as it's not that critical. A new Bioc release is coming soon anyway. As for the devel version, I'm guessing this is more to your liking: > session <- browserSession("UCSC") > q2 <- ucscTableQuery(session, "all_mrn ...
written 10.2 years ago by Michael Lawrence620
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Answer: A: rtracklayer issue (getTable)
... On Thu, Oct 1, 2009 at 11:47 PM, Mark Robinson wrote: > Hello BioC list. > > I've encountered a small problem when trying to download some tracks from > UCSC with rtracklayer. Specifically, I'm trying to get the "mrna" table. > The example below works great for the "refGene" table, ...
written 10.2 years ago by Michael Lawrence620
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Answer: A: a little error in 'rtracklayer' vignette
... This was a bug in rtracklayer itself, not the vignette. It's fixed in 1.5.16. Thanks, Michael On Thu, Sep 24, 2009 at 8:53 PM, LiGang wrote: > > > Following code were taken from the 'rtracklayer' vignette, and will lead to > an > error message: > > #========================= ...
written 10.2 years ago by Michael Lawrence620
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Answer: A: browserView does not work in 'rtracklayer' [failure to coerce "CompressedInteger
... Thanks for bringing this IRanges change to my attention. Fixed in 1.5.15. On Tue, Sep 22, 2009 at 12:11 AM, LiGang wrote: > > browserView does not work in 'rtracklayer' [failure to > coerce "CompressedIntegerList"] > > > library(rtracklayer) > browserSession("UCSC")->sessi ...
written 10.2 years ago by Michael Lawrence620
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Comment: C: can not coerce CompressedIntegerList to vector or integer in 'IRanges' package
... On Tue, Sep 22, 2009 at 7:35 AM, Patrick Aboyoun wrote: > LiGang, > The unlist command will get you what you are looking for. AtomicList > objects should be thought of as typed lists (as.integer on a regular list > containing integer elements will also throw an error). Calling as.int ...
written 10.2 years ago by Michael Lawrence620
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Answer: A: "rtracklayer" is not compatible with the lateset "IRanges" package
... Have you tried reinstalling rtracklayer? Michael On Wed, Sep 16, 2009 at 8:14 PM, LiGang wrote: > > the newest "rtracklayer" and "IRanges" packages are not compatible, is it > because class "ANYTHING" is not defined in package "IRanges" since version > 1.3.73 anymore? > > libra ...
written 10.2 years ago by Michael Lawrence620
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Comment: C: Merging RandData object with names on the IRanges part
... On Thu, Aug 20, 2009 at 8:33 AM, Michael Dondrup < Michael.Dondrup@bccs.uib.no> wrote: > Hi Ulrike, > > I think you can use function c(). > you then can get the IRanges names preserved in your examples: > > > ranges(c(t1,t2))[[3]] > IRanges object: > start e ...
written 10.3 years ago by Michael Lawrence620
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Comment: C: BED15 format for rtracklayer
... Just put "color" as a column in the RangedData. It can be in any format accepted by col2rgb(). Michael On Wed, Aug 5, 2009 at 7:08 AM, rcaloger wrote: > Thanks for the info related to the RGB feature I completely missed that > point when I red the BED format help on the UCSC browser. > C ...
written 10.4 years ago by Michael Lawrence620
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Comment: C: BED15 format for rtracklayer
... On Tue, Aug 4, 2009 at 11:16 AM, rcaloger wrote: > The BED15 format is quite nice to represent alternative splicing events > data (insertion/skipping), the grey scale of the score from the BED format > is not ideal. Now, thanks to your implementation of BED15 format I can > update the ...
written 10.4 years ago by Michael Lawrence620

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