... Dario Strbenac writes:
> Is there a way to move BSgenome.Hsapiens.UCSC.hg19 from an R 2.15
to an R 3.0 library without
> downloading it all again ? I installed it as a Windows binary.
If so, I w ...
Subset replacement like this
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
DataFrame with 2 rows and 2 columns
... 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
> the letter (quite literally). In step "e" I paste the example
> into myFile ...
I was expecting rd[ -1 , ] to be a RangedData object that contained
but the first row:
> rd <-
> rd[['one']] <- 'one'
> rd[1:2,] # OK
RangedData with 2 rows and 1 value column across 4 spaces
space r ...
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) )
> x <- rep(1:4,c(1,2,1,2))
'integer' Rle of length 16 with 4 runs
Lengths: 1 4 3 8
Values : 1 2 3 4
... On Tue, 1 Dec 2009, Patrick Aboyoun wrote:
> Thanks for the speedup to coverage for large width IRanges objects.
> 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 ...
The semantics of the IRanges package and especially the RangedData
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 ...
... Janet Young writes:
> 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
> individually (i.e. NOT corrected ...
... 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 ...
You used method='cat.stat', which is (only) suitable for SNPs, I
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
- i.e. you would have to **call** the SNPs. (And reasonably enough,