search for: apcluster

Dear colleagues, This is to inform you that Version 1.3.0 of the R package apcluster has been released on CRAN yesterday. We did a major extension and overhaul of the package. Most importantly, we added Leveraged Affinity Propagation in fulfillment of multiple users requests. It should now be much easier to cluster large data sets. Apart from this extension, the interfaces to...

Hi, I was wondering how it was possible to access the actual cluster exemplars from the APResult class. Currently it only spits it out onto the terminal if you type the object but there is no other way to see which one is the examplar. Would appreciate any help. Thanks, Sachin [[alternative HTML version deleted]]

Dear colleagues, This is to inform you that Version 1.3.1 of the R package apcluster has been released on CRAN. We did a major improvement of heatmap and dendrogram plotting, as well as several minor improvements of the package. For more details, see the following URLs: http://www.bioinf.jku.at/software/apcluster/ http://cran.r-project.org/web/packages/apcluster/index.html Bes...

Dear colleagues, This is to inform you that I will be giving a webinar on the apcluster package on Thursday, June 13, 2013, 7:00pm CEST (10:00am PDT). The outline of the one-hour webinar is as follows: - Introduction to affinity propagation (AP) clustering - The apcluster package, its algorithms, and visualization tools - Live apcluster demonstration - Question and Answer period T...

...seems I have three options: > > 1) not supplying the sort() function yet (it is not yet in the release, > but only in my internal devel version) > 2) including a dependency to BiocGenerics > 3) leaving the problem open, mentioning in the documentation that users > who want to use apcluster in conjunction with Bioconductor should load > BiocGenerics first 4) define an S3 method, as mentioned in my previous post H. > > As far as I got it, there seems to be no other clean way to get rid of > the problem, right? > > Best regards, > Ulrich > > > On 03/26/2...

...t;> bodenhofer@bioinf.jku.at >> > wrote: >> >> > [cross-posted to R-devel and bioc-devel] >> > >> > Hi, >> > >> > I am trying to implement a 'sort' method in one of the CRAN packages I >> am >> > maintaining ('apcluster'). I started with using setMethod("sort", ...) >> in >> > my package, which worked fine. Since many users of my package are from >> the >> > bioinformatics field, I want to ensure that my package works smoothly >> with >> > Bioconductor. Th...

...ge. For the time being, it seems I have three options: 1) not supplying the sort() function yet (it is not yet in the release, but only in my internal devel version) 2) including a dependency to BiocGenerics 3) leaving the problem open, mentioning in the documentation that users who want to use apcluster in conjunction with Bioconductor should load BiocGenerics first As far as I got it, there seems to be no other clean way to get rid of the problem, right? Best regards, Ulrich On 03/26/2014 02:44 PM, Michael Lawrence wrote: > That might be worth thinking about generally, but it would still...

...er at bioinf.jku.at> > To: Prof Brian Ripley <ripley at stats.ox.ac.uk> > CC: [...stripped for the sake of privacy ...] > > > > Dear Prof. Ripley, > > Thank you very much for bringing this important issue to my attention. I > am the maintainer of the 'apcluster' package. My package refers to > 'Biostrings' in an example section of a help page (a quite insignificant > one, by the way), which creates errors on some platforms. It also refers > to 'kebabs' in the package vignette, which leads to warnings. > > I could fix the...

...t;> >> ??????? CC:? ? ?[...stripped for the sake of privacy ...] >> >> >> >> ??????? Dear Prof. Ripley, >> >> ??????? Thank you very much for bringing this important issue to my >> ??????? attention. I >> ??????? am the maintainer of the 'apcluster' package. My package >> refers to >> ??????? 'Biostrings' in an example section of a help page (a quite >> ??????? insignificant >> ??????? one, by the way), which creates errors on some platforms. It >> ??????? also refers >> ??????? to 'kebabs&...

[cross-posted to R-devel and bioc-devel] Hi, I am trying to implement a 'sort' method in one of the CRAN packages I am maintaining ('apcluster'). I started with using setMethod("sort", ...) in my package, which worked fine. Since many users of my package are from the bioinformatics field, I want to ensure that my package works smoothly with Bioconductor. The problem is that the BiocGenerics package also redefines 'so...

...:40 +0100 From: Ulrich Bodenhofer <bodenhofer at bioinf.jku.at> To: Prof Brian Ripley <ripley at stats.ox.ac.uk> CC: [...stripped for the sake of privacy ...] Dear Prof. Ripley, Thank you very much for bringing this important issue to my attention. I am the maintainer of the 'apcluster' package. My package refers to 'Biostrings' in an example section of a help page (a quite insignificant one, by the way), which creates errors on some platforms. It also refers to 'kebabs' in the package vignette, which leads to warnings. I could fix the first, more severe, pro...

...lt;mailto:ripley at stats.ox.ac.uk>> > CC:? ? ?[...stripped for the sake of privacy ...] > > > > Dear Prof. Ripley, > > Thank you very much for bringing this important issue to my > attention. I > am the maintainer of the 'apcluster' package. My package refers to > 'Biostrings' in an example section of a help page (a quite > insignificant > one, by the way), which creates errors on some platforms. It > also refers > to 'kebabs' in the package vignette,...

Hi, I have a 1.000 observations with 10 attributes (of different types: numeric, dicotomic, categorical ecc..) and a measure M. I need to cluster these observations in order to assign a new observation (with the same 10 attributes but not the measure) to a cluster. I want to calculate for the new observation a measure as the average of the meausures M of the observations in the cluster

...ons: >> >> 1) not supplying the sort() function yet (it is not yet in the release, >> but only in my internal devel version) >> 2) including a dependency to BiocGenerics >> 3) leaving the problem open, mentioning in the documentation that users >> who want to use apcluster in conjunction with Bioconductor should load >> BiocGenerics first > > 4) define an S3 method, as mentioned in my previous post > > H. > After a while, I came back to this suggestion. Thanks, Herv?! I now tried it and it indeed works smoothly: all problems I mentioned - as you...

CRAN (and crantastic) updates this week New packages ------------ * apcluster (1.0.1) Ulrich Bodenhofer http://crantastic.org/packages/apcluster The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are analogous to the Matlab code published by Frey and Dueck. * BioPhysConnectoR (1.6-1) Franziska Hoffga...

I'm in the process of converting some S3 methods to S4 methods. I have this function : setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")}) setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) { ... ... ... })