search for: hopach

Displaying 14 results from an estimated 14 matches for "hopach".

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2008 Jan 25
3
Help
Hi, I got command to execute R code from Mark. but it was showing error.. Error in library(hopach) : there is no package called 'hopach' Does it mean this library hopach is not installed. But I have installed complete Bioconductor package. I am confused. can you help me in this thanks Regards, -- Prateek Singh Final year Bioinformatics(BTech) Vellore Institute Of Technology Vellore-...
2007 Jul 23
2
persp and greek symbols in the axes labels
Hello, I am plotting a 3D function using persp and I would like to use greek symbols in the axes labels. I have found examples like this one on the web: plot(0,0,xlab=expression(kappa[lambda]),ylab=substitute(paste(phi,"=",true,sigma),list(true=5))) this works well with plot but not with persp: with the command persp(M,theta = -20,phi =
2008 Jan 25
1
How to execute R code
Hi, I have 'R' code in file. saved it as exmaple.r here is the code....... library("hopach") GSE <- read.table("gene_expression_data",sep="\t",header=TRUE,row.names=TRUE) gene.dist <- distancematrix(t(GSE),d="euclid") gene.hobj <- hopach(t(GSE), dmat=gene.dist, mss="med") labelstosil(gene.hobj$cluster$label,gene.dist) I dont know ho...
2011 Aug 08
3
Distance between a vector and matrix rows
I am trying to find the distance between a vector and each row of a dataframe. I am using the function "distancevector" in the package "hopach" as follows: mydata<-as.data.frame(matrix(c(1,1,1,1,0,1,1,1,1,0),nrow=2)) V1 V2 V3 V4 V5 1 1 1 0 1 1 2 1 1 1 1 0 vec <- c(1,1,1,1,1) d2<-distancevector(mydata,vec,d="euclid") The Euclidean distance between the two rows of the data frame to the vector should be...
2006 Nov 30
3
newbie: new_data_frame <- selected set of rows
...ling data my_dataframe I calculate distances. order them then extract top five hits my_dataframe <- read.table("myDB.csv", header=F, dec=".", sep=";", row.names=1) #reads the whole file scaled_DB <- scale(my_dataframe, center=FALSE) #scales the values require(hopach) #checks necessary R package distances <- order(distancevector(scaled_DB, scaled_DB['query',], d="euclid")) #calculates distances and orders the results from lowest for(i in distances[1:5]) print( dbfile[i,]) #prints top five hits just for debugging What I want to do: 1) cr...
2005 Nov 05
2
problem with the assignment function
...04524671 > sessionInfo() R version 2.2.0, 2005-10-06, i686-pc-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: fineld hopach cluster fields lattice "1.0.0" "1.2.1" "1.10.2" "2.0" "0.12-9" Any hint or suggestions will be much appreciated. Yan [[alternative HTML version deleted]]
2006 Feb 27
1
about clustering method
...ist of the algorithms I found. But I'm not sure if It's the complete list. Could you please check it and see if there're other ones? Thank you very much! P.S.: List of the algorithms related to clustering: (1) Hierarchical methods hclust agnes diana mona mclust hopach (2) Partitioning methods pam: clustering around medoids clara: clustering large datasets fanny: fuzzy cluster analysis (3) k-means: bdCluster: big data k-means clustering kmeans: Hartigan's K-Means Clustering [[alternative HTML version deleted]]
2006 Nov 30
0
new_data_frame <- selected set of rows
...ling data my_dataframe I calculate distances. order them then extract top five hits my_dataframe <- read.table("myDB.csv", header=F, dec=".", sep=";", row.names=1) #reads the whole file scaled_DB <- scale(my_dataframe, center=FALSE) #scales the values require(hopach) #checks necessary R package distances <- order(distancevector(scaled_DB, scaled_DB['query',], d="euclid")) #calculates distances and orders the results from lowest for(i in distances[1:5]) print( dbfile[i,]) #prints top five hits just for debugging What I want to do: 1) cr...
2008 Feb 22
0
How to get MSS value for individual clusters.
Hi there, I am working on clustering genomic data. I am using HOPACH method for clustering. I have a query here. How can i get SS (split silhouette) value for individual clusters. What I am getting as MSS value, is Mean of all SS value of individual cluster. Hence I am getting single value for a gene set. But I would be very helpful for me if I get silhouette valu...
2006 Mar 17
0
(no subject)
...P.S.: List: Appropriate for large data set: clara: k-mean mclust: fits mixtures of Gaussians using the EM algorithm clue: implements ensemble methods for both hierarchical and partitioning cluster methods. cmeans: Fuzzy clustering bclust: bagged clustering hopach: a hybrid between hierarchical methods and PAM and builds a tree by recursively partitioning a data set. som: Self-organizing maps are available Not appropriate for large data set: (a) Hierarchical clustering: not appropriate for large data set because of the qua...
2010 Aug 25
1
Documenting S4 Methods
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, ...) { ... ... ... })
2007 Oct 30
6
trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64
I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is
2007 Mar 26
1
Problem in loading all packages all at once
...oc","haplo.ccs","haplo.stats","hapsim","hddplot","hdf5","hdrcde","hett","HI","hier.part","hierfstat","HighProbability","Hmisc","hmm.discnp","homals","hopach","howmany","HSAUR","HTMLapplets","httpRequest","hwde","hybridHclust","HyperbolicDist","ICE","Icens","IDPmisc","ifs","igraph","iid.test","impute","ine...
2010 Jul 18
6
CRAN (and crantastic) updates this week
...tools (0.21), gRain (0.8.5), grImport (0.6-1), gss (1.1-5), gsubfn (0.5-3), gtools (2.6.2), gWidgets (0.0-41), gWidgetsRGtk2 (0.0-67), gWidgetsrJava (0.0-19), gWidgetstcltk (0.0-38), gWidgetsWWW (0.0-19), hapassoc (1.2-4), hash (2.0.1), hergm (1.2-5), hglm (1.1.1), highlight (0.2-1), Hmisc (3.8-2), hopach (2.9.1), ibr (1.2.2), identity (0.2-1), ifultools (1.0-7), imprProbEst (1.0.1), impute (1.22.0), imputeMDR (1.1), inline (0.3.5), inlinedocs (1.1), intamapInteractive (1.0-9), intervals (0.13.2), introgress (1.2.3), ipw (1.0-5), isa2 (0.2.1), ismev (1.35), isopam (0.9-8), kernlab (0.9-10), kmi (0.3...