search for: clvalid

Dear all, I am encountering a cyclic dependency error when running R CMD check on an R package I wrote (R version 2.6.1, Mac OS X 10.4), see the error message below. Creating a new generic function for "print" in "clValid" Creating a new generic function for "summary" in "clValid" Creating a new generic function for "plot" in "clValid" Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) : cyclic name space dependencies are not su...

...ed Warning: cannot remove prior installation of package 'cluster' updating HTML package descriptions > load(cluster) Error en load(cluster) : objeto 'cluster' no encontrado > library(cluster) Error en library(cluster) : there is no package called 'cluster' > library(clValid) Loading required package: cluster Error: package 'cluster' could not be loaded Además: Warning message: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'cluster' > update.packages() --- Please select a CRAN mirror f...

...or the Fedora checks on R-devel. As >> you can see from the CRAN results pages (at least at the time of writing), >> packages >> >> ACMEeqtl BoSSA CNVassoc CorShrink GRANBase GenCAT GiANT NMF PlackettLuce >> ProFit ProFound RNAseqNet SIBERG antaresRead apcluster cherry clValid coloc >> colorhcplot entropart filematrix fuzzyforest fuzzyjoin glycanr hexbin loon >> nscancor ordinalgmifs penalized phangorn propr shiftR switchr tcgsaseq >> tileHMM tmod >> >> then give ERRORs or (new) WARNINGs on their checks. Please correct ASAP, >> and by...

...sic question: Is it correct to assume that when using cutree to set the # clusters (say k=4), cutree determines the clusters by the largest distances among all potential clusters? I've read the R help for cutree and am using it to define the number of groups to obtain Dunn Index scores (using clValid library) for cluster analysis (using Euclidean Distance and Ward's method) More specific (if helpful): I understand that cutree is used to set the number of clusters for which the Dunn Index will base it's score on. But the r help doesn't explain how the groups are determined. Prior t...

...gt;> ??????????? CRAN results pages (at least at the time of writing), >> packages >> >> ??????????? ACMEeqtl BoSSA CNVassoc CorShrink GRANBase GenCAT GiANT >> ??????????? NMF PlackettLuce ProFit ProFound RNAseqNet SIBERG >> ??????????? antaresRead apcluster cherry clValid coloc colorhcplot >> ??????????? entropart filematrix fuzzyforest fuzzyjoin glycanr hexbin >> ??????????? loon nscancor ordinalgmifs penalized phangorn propr shiftR >> ??????????? switchr tcgsaseq tileHMM tmod >> >> ??????????? then give ERRORs or (new) WARNINGs on the...

...to use it for the Fedora checks > on R-devel. As you can see from the CRAN results pages (at least at > the time of writing), packages > > ACMEeqtl BoSSA CNVassoc CorShrink GRANBase GenCAT GiANT NMF > PlackettLuce ProFit ProFound RNAseqNet SIBERG antaresRead apcluster > cherry clValid coloc colorhcplot entropart filematrix fuzzyforest > fuzzyjoin glycanr hexbin loon nscancor ordinalgmifs penalized phangorn > propr shiftR switchr tcgsaseq tileHMM tmod > > then give ERRORs or (new) WARNINGs on their checks.? Please correct > ASAP, and by Feb 20 to safely retain t...

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

...vel. As you can see from the > CRAN results pages (at least at the time of writing), packages > > ACMEeqtl BoSSA CNVassoc CorShrink GRANBase GenCAT GiANT > NMF PlackettLuce ProFit ProFound RNAseqNet SIBERG > antaresRead apcluster cherry clValid coloc colorhcplot > entropart filematrix fuzzyforest fuzzyjoin glycanr hexbin > loon nscancor ordinalgmifs penalized phangorn propr shiftR > switchr tcgsaseq tileHMM tmod > > then give ERRORs or (new) WARNINGs on their checks.? >...

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, ...) { ... ... ... })