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
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
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
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
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
matrix
1 1 3
2 2 4
3 1 3
4 2 4
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
matrix
Hi Martin,
Thanks for the fix, I'll check it out.
jim
On Tue, May 20, 2014 at 12:35 PM, Martin Morgan mtmor...@fhcrc.org 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
Fixed in release and devel (IRanges).
Thanks,
Michael
On Tue, May 20, 2014 at 1:22 AM, Julian Gehring julian.gehr...@embl.dewrote:
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
Regarding the following extract of ?options:
‘editor’: a non-empty string, or a function that is called with a
file path as argument.
edit.default currently calls the function with three arguments: name,
file, and title. For example, running the following
vimCmd - 'vim -c set
Version 3.1.0 of R has imposed a very small data limit on writing to fifos on
Linux. Consider the following R code (Assumes that ff is a fifo in the R
process's current directory):
con - fifo(ff, a+b)
writeBin(raw(12501), con)
In R 3.0.3, this returns without error and the data is available on
It _was_ part of the fifo for Windows patch. As if does not seem to be
needed for Windows, it has been reverted.
On 20/05/2014 16:02, James Smith wrote:
Version 3.1.0 of R has imposed a very small data limit on writing to fifos on Linux.
Consider the following R code (Assumes that ff is a
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