Hi Herve,
I must retract my previous statement about 'yieldSize' and 'which'. As
of Rsamtools 1.15.0, scanBam() (and functions that build on it) does
handle the case where both are supplied. This is true for the non-mate
and mate-pairing code.
From ?BamFile:
yieldSize: Number of rec
Fixed in 1.21.38.
On Fri, Mar 28, 2014 at 9:15 AM, Leonard Goldstein <
goldstein.leon...@gene.com> wrote:
> Dear Bioc developers,
>
> I ran into problems when using the flank function with the start
> argument set to a named vector.
>
> This returns an IRanges with named starts and ends, which c
Thanks, should be resolved in 1.23.20 (devel).
On Fri, Mar 28, 2014 at 8:09 AM, Julian Gehring wrote:
> Hi,
>
> Exporting a GRanges object to the 'bigwig' format with rtracklayer fails
> if not all seqlevels are used:
>
> #+BEGIN_SRC R
> library(rtracklayer)
> library(GenomicRanges)
>
> ##
Dear Bioc developers,
I ran into problems when using the flank function with the start
argument set to a named vector.
This returns an IRanges with named starts and ends, which causes
problems downstream. Please see example below.
Thanks for your help
Leonard
> ir <- IRanges(1, 1)
> fl <- fla
Hi,
Exporting a GRanges object to the 'bigwig' format with rtracklayer fails
if not all seqlevels are used:
#+BEGIN_SRC R
library(rtracklayer)
library(GenomicRanges)
## example data
example(GRanges)
lg = reduce(unstrand(longGR))
lg$score = 1:6
## full one works
export(lg, tempfi
