hi,
I came across an error in trying to subset a GRangesList with metadata
columns on the metadata columns:
> library(GenomicRanges)
> grl <- GRangesList(GRanges(),GRanges())
> mcols(grl) <- DataFrame(a=1:2)
> mcols(mcols(grl)) <- DataFrame(type="z")
> grl[1:2]
Error in normalizeSingleBracke
Hi all,
I used to be able to do this:
as.data.frame(DataFrame(), stringsAsFactors=TRUE)
now I get a warning:
Warning in as.data.frame(DataFrame(), stringsAsFactors = TRUE) :
Arguments in '...' ignored
Do I have the guarantee nowadays that coercing a DataFrame to a data.frame does
not cast cha
Hi Marc,
I saw these warnings in Gviz, but they stem from GenomicFeatures
Warning messages:
1: 'isActiveSeq' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and help("GenomicFeatures-deprecated").
2: 'isActiveSeq' is deprecated.
Use 'seqlevels' instead.
See help("Deprecated") and he
Hi Florian,
Yes we are trying to make things more uniform. seqlevels() lets you
rename as well as deactivate chromosomes you want to ignore, so it was
really redundant with isActiveSeq(). So we are moving away from
isActiveSeq() just so that users have less to learn about. The reason
why is
On Fri, Sep 13, 2013 at 7:35 AM, Hahne, Florian
wrote:
> Hi all,
> I used to be able to do this:
> as.data.frame(DataFrame(), stringsAsFactors=TRUE)
>
> now I get a warning:
> Warning in as.data.frame(DataFrame(), stringsAsFactors = TRUE) :
> Arguments in '...' ignored
>
> Do I have the guarant
Yes I try to get updates on everything every time.
Marc
On 09/12/2013 10:38 AM, Kasper Daniel Hansen wrote:
> Ok, sounds good.
>
> This is especially nice to know for the annotation packages which are
> "hand" created as opposed to being created by some script.
>
> Kasper
>
>
> On Thu, Sep
