Hi Aaron,
On 11/16/2015 09:39 AM, Hervé Pagès wrote:
Hi Aaron,
On 11/15/2015 12:37 PM, Aaron Lun wrote:
Hi Herve,
I would have expected GRanges behaviour, where the metadata is affected
by the replacement. For example, with GRanges objects, I often use the
metadata to store statistics or desc
Hello,
How does your package differ to importing GSE62944 into R with AnnotationHub
http://bioinformatics.oxfordjournals.org/content/31/22/3666.long ? It seems
like unnecessary duplication.
--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 205
Hi Marcin,
It's technically possible to change the name. In order to try to keep
this the less disruptive, we would only do this in devel and we would
need to create a new package there by cloning the current package and
changing its name. Then we would add a deprecation/redirection message
in th
Hi Aaron,
On 11/15/2015 12:37 PM, Aaron Lun wrote:
Hi Herve,
I would have expected GRanges behaviour, where the metadata is affected
by the replacement. For example, with GRanges objects, I often use the
metadata to store statistics or descriptors relevant to each genomic
interval, e.g., peak s
I have published `RTCGA.rnaseq` R package that provides datasets from TCGA
project containig RNA sequencing (gene's expressions). I am wondering if
there is a way to change this package name to be more proper like
`RTCGA.RNAseq` and if that's possible, how should I do that and to whom
should I writ
While I'm on this point, there's another, more subtle issue with using
sparseMatrix(). Specifically, there's a distinction between zeros and
missing values when considering a ContactMatrix. For example, in Hi-C
data, a zero in the matrix means there aren't any read pairs mapping
between the cor
Thanks for the comment Nadhir.
I had considered the use of a sparse matrix class. The reason I didn't
implement it originally is because truly sparse interaction data would
be better represented by just working with the pairwise format in the
InteractionSet. You need the row/column indices to
Hello all,
I thought I might give an update on the state of affairs for the
InteractionSet package. Currently, there's three classes:
- the GInteractions class, inheriting from Vector and intended to
represent pairwise interactions between genomic regions (based on
suggestions from Malcolm P
