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