User: Charles Berry

gravatar for Charles Berry
Charles Berry290
Reputation:
290
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Trusted
Location:
United States
Last seen:
3 months, 2 weeks ago
Joined:
16 years, 8 months ago
Email:
c******@ucsd.edu

Professor Emeritus of Biostatistics and Bioinformatics

Current interest: statistical models, methods, and software for exploring populations of integration sites such as occur in retroviral infections or in gene therapies using retrovirus-like constructs.

 

Posts by Charles Berry

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Is there a package to convert DNA coordinates to Cytogenetic location?
... biovizBase. `example("getIdeoGR" )` is a start. ...
written 3 months ago by Charles Berry290
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Answer: A: How to get duplicate IDs numbered?
... ave() will give the sequential numbers, so something like with(mydf, paste0(ID, ave( ID, ID, FUN=seq_along ))) should do it.   ...
written 3.9 years ago by Charles Berry290
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Comment: C: Problems updating Bioconductor with R 3.2.0
... No. There was a post on bio-devel. Try remove.packages("BiocInstaller"). Then start over. ...
written 4.3 years ago by Charles Berry290
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Comment: C: initializing DirichletMultinomial::dmn
... On Fri, 11 Jul 2014, Martin Morgan wrote: > On 07/10/2014 02:45 PM, Charles Berry wrote: >> >> I'd like to be able to specify the starting 'centers' for dmn(). >> [snip] > I'll look into this, thanks for the suggestion. Is there a more general issue > that makes the ran ...
written 5.0 years ago by Charles Berry290
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initializing DirichletMultinomial::dmn
... I'd like to be able to specify the starting 'centers' for dmn(). Details: IIUC DirichletMultinomial::dmn(count, k) will initialize the EM algorithm using a kmeans heuristic for selecting the starting point. Replicate runs on the same data can yield stark differences in the result. I have a datas ...
written 5.0 years ago by Charles Berry290 • updated 5.0 years ago by Martin Morgan ♦♦ 23k
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Most efficient way to compute width of overlap of multiple features
... Michael Lawrence writes: > Thanks for your reply and for GenomicRanges. Please see inline comments below. > > On Tue, Jan 7, 2014 at 9:30 AM, Charles Berry wrote: > > > Vince S. Buffalo ...> writes: > > > > > > > > Hi Bioconductor folks, > > ...
genomicranges written 5.5 years ago by Charles Berry290 • updated 5.5 years ago by Michael Lawrence11k
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Most efficient way to compute width of overlap of multiple features
... Vince S. Buffalo writes: > > Hi Bioconductor folks, > > I'm trying to create some GRanges summaries, but I think I may be missing > an obvious solution. I have fixed-width windows as a GRanges object, and > for each window/row I'd like to add a metadata column that indicates how ...
written 5.5 years ago by Charles Berry290 • updated 5.5 years ago by Michael Lawrence11k
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Answer: A: Getting first or last hit from a Hits object
... Peter Hickey writes: > > Hi all, > > Suppose I've created a Hits object by > all_hits <- findOverlaps(query, subject, select = 'all', type = 'any') > and now I want to get the first (or last) hit for each query. Of course, > [...] gr1 <- GRanges(rep(letters,each=10), ...
written 5.8 years ago by Charles Berry290
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Answer: A: coverage() in IRanges gives >0 coverage when weight == 0
... Ludo Pagie writes: > > Hi all, > > I don't understand what's going on here.I'm trying to compute the > coverage of a few ranges. I specify a weight for these ranges and for > some positions I get a coverage even though I know these positions are > only covered by ranges which ...
written 5.9 years ago by Charles Berry290
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Answer: A: saving GRanges objects - resulting file size issue
... Valerie Obenchain writes: > > Hi Andrew, > > I can't reproduce this problem. Can you successfully save the files in a > different order, i.e., is it just the addition of 'introns' that is > giving you trouble? > > I assume these are custom annotation GRanges that did not co ...
written 5.9 years ago by Charles Berry290

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Popular Question 3.9 years ago, created a question with more than 1,000 views. For Most efficient way to compute width of overlap of multiple features
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