Fixed in release and devel (IRanges).
Thanks,
Michael
On Tue, May 20, 2014 at 1:22 AM, Julian Gehring wrote:
> Hi,
>
> If I want to bind two GRanges object with a matrix in the meta columns,
> the concatenation of the two fails in bioc-stable (GenomicRanges 1.16.3)
> and bioc-devel (GenomicRang
Hi Martin,
Thanks for the fix, I'll check it out.
jim
On Tue, May 20, 2014 at 12:35 PM, Martin Morgan wrote:
> On 05/13/2014 08:17 AM, James Bullard wrote:
>
>> Hi Martin, thanks for the quick response. The data is certainly
>> shareable. Here
>> is a link to a bam + bai + sam file that I hav
On 05/20/2014 12:49 PM, Hervé Pagès wrote:
Hi Julian,
At the root of the problem is what rbind() does on DataFrames containing
matrices:
m <- matrix(1:4, nrow=2)
df <- DataFrame(m=I(m))
df2 <- rbind(df, df)
Then:
> df2
DataFrame with 8 rows and 1 column
m
Hi Julian,
At the root of the problem is what rbind() does on DataFrames containing
matrices:
m <- matrix(1:4, nrow=2)
df <- DataFrame(m=I(m))
df2 <- rbind(df, df)
Then:
> df2
DataFrame with 8 rows and 1 column
m
1 1 3
2 2 4
3 1 3
4 2 4
On 05/13/2014 08:17 AM, James Bullard wrote:
Hi Martin, thanks for the quick response. The data is certainly shareable. Here
is a link to a bam + bai + sam file that I have been using for benchmarking:
https://www.dropbox.com/s/eat31mnmmco1zoh/example-bam.tar.bz2
There is a method in SAM to elid
if living, the time-to-death usually refers to last follow-up time. it's
just censored in cox model.
However, the first patient example indeed looks suspicious to me:
days_to_death vital_status
days_to_tumor_recurrence
TCGA.20.0990 789 living
Hej Keith!
I agree that this would be useful. For having been very close to the 2004
attempt - a then colleague of mine set up a solution similar to what you
describe - I can tell you that the main reason for it dying out was that
despite advertising it, it never got widely used. I don’t know w
Hello all,
I was wondering if there had been any progress towards adopting a bug
tracking system for Bioconductor?
It has been discussed at least a couple times in the past, e.g.:
- https://stat.ethz.ch/pipermail/bioc-devel/2011-October/002844.html
- https://stat.ethz.ch/pipermail/bioc-d
library("curatedOvarianData")
data(TCGA_eset)
clinical <- pData(TCGA_eset)[, 1:20]
alive <- clinical[clinical[, "vital_status"] == "living", ]
head(alive[, c("days_to_death", "vital_status", "days_to_tumor_recurrence")])
days_to_death vital_status days_to_tumor_recurrence
TCGA.20.0990
Hi,
If I want to bind two GRanges object with a matrix in the meta columns,
the concatenation of the two fails in bioc-stable (GenomicRanges 1.16.3)
and bioc-devel (GenomicRanges 1.17.13) with:
'''
Error in validObject(.Object) :
invalid class “GRanges” object: number of rows in DataTable
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