User: Charles Berry

gravatar for Charles Berry
Charles Berry290
Reputation:
290
Status:
Trusted
Location:
United States
Last seen:
4 months, 3 weeks ago
Joined:
16 years, 9 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 2 of 3 • next >
0
votes
2
answers
473
views
2
answers
Answer: A: Migrating a Large BSgenome Package to R 3.0
... Dario Strbenac writes: > > Is there a way to move BSgenome.Hsapiens.UCSC.hg19 from an R 2.15 library to an R 3.0 library without > downloading it all again ? I installed it as a Windows binary. > Maybe http://article.gmane.org/gmane.comp.lang.r.devel/33286 will help? If so, I w ...
written 6.3 years ago by Charles Berry290
0
votes
1
answer
534
views
1
answer
DataFrame bug?
... >> Subset replacement like this df['a','c2']<-3 depends on the position of row 'a' when 'c2' is a new column. Row 'a' first: > df1 <- DataFrame(c1=1:2,row.names=c("a","b")) > df1['a','c2'] <- 3 > df1 DataFrame with 2 rows and 2 columns c1 c2 a ...
written 6.5 years ago by Charles Berry290 • updated 6.5 years ago by Valerie Obenchain6.7k
0
votes
2
answers
609
views
2
answers
Answer: A: Biostrings C interface :: example not compiling
... On Fri, 2 Apr 2010, Erik Wright wrote: > Hello all, > > I am trying to interface Biostrings from C for the first time. I > followed the example given in the header of Biostrings_interface.h to > the letter (quite literally). In step "e" I paste the example function > into myFile ...
written 9.4 years ago by Charles Berry290
0
votes
1
answer
439
views
1
answer
RangedData negative row subscript
... I was expecting rd[ -1 , ] to be a RangedData object that contained all but the first row: > rd <- RangedData(IRanges(start=1:20,width=2),space=rep(letters[1:4],5)) > rd[['one']] <- 'one' > rd[1:2,] # OK RangedData with 2 rows and 1 value column across 4 spaces space r ...
written 9.6 years ago by Charles Berry290 • updated 9.6 years ago by Michael Lawrence11k
0
votes
0
answers
431
views
0
answers
unexpected result of rep(Rle(), times=<vector or Rle>)
... Using IRanges_1.4.0 here (checked elsewhere with 1.4.8): I would expect rep( Rle(x), times=Rle(x) ) == Rle( rep(x, x) ) but > x <- rep(1:4,c(1,2,1,2)) > Rle(rep(x,x)) 'integer' Rle of length 16 with 4 runs Lengths: 1 4 3 8 Values : 1 2 3 4 > rep(Rle(x),times=Rle(x)) ...
written 9.6 years ago by Charles Berry290
0
votes
1
answer
570
views
1
answers
Answer: A: IRanges:::coverage() speedup/enchancement
... On Tue, 1 Dec 2009, Patrick Aboyoun wrote: > Chuck, > Thanks for the speedup to coverage for large width IRanges objects. I checked > in changes to IRanges 1.5.13 in BioC 2.6 (for use with R-devel) based on the > code you submitted. I'll back port this code to BioC 2.5 (R 2.10) in the n ...
written 9.7 years ago by Charles Berry290
0
votes
1
answer
401
views
1
answer
IRanges:::coverage() speedup/enchancement
... The semantics of the IRanges package and especially the RangedData class are very apprpriate for some of the applications I deal with. Unfortunately, coverage() is too slow to be useful to me. I wonder if the Biocore Team would consider retooling it to make it faster? Below I provide a link to a ...
coverage iranges written 9.7 years ago by Charles Berry290 • updated 9.7 years ago by Michael Lawrence620
0
votes
2
answers
761
views
2
answers
Answer: A: understanding GOstats p-value
... Janet Young writes: > > Hi, > > I have a fairly naive question - I want to make sure I can more or > less understand the p-values that GOstats hyperGTest comes out with. > Am I right in thinking the p-value is for enrichment of each category > individually (i.e. NOT corrected ...
written 11.6 years ago by Charles Berry290
0
votes
1
answer
459
views
1
answers
Answer: A: microarray data and survival analysis
... On Tue, 20 Feb 2007, Dr_Gyorffy_Balazs wrote: > Dear All! > > I have microarray data for cancer patients and I want to correlate the genes with survival. > One option is the survival analysis of the PAM package. However, only the windows EXCEL version offers this option, but the packa ...
written 12.5 years ago by Charles Berry290
0
votes
4
answers
460
views
4
answers
Answer: A: Communicating gene-probe relationships to sam
... Charles, You used method='cat.stat', which is (only) suitable for SNPs, I think. This seems like an odd choice for detecting SFPs. You would have to do more work to get this to work properly if you actually were counting SNPs - i.e. you would have to **call** the SNPs. (And reasonably enough, sa ...
written 13.3 years ago by Charles Berry290

Latest awards to Charles Berry

Popular Question 4.0 years ago, created a question with more than 1,000 views. For Most efficient way to compute width of overlap of multiple features
Autobiographer 4.8 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 140 users visited in the last hour