[R] Hierarchical Clustering in R

[Serpil ŞEN]

Dear Authorized Sir / Madam,

I need your help on clustering with R.

I have symmetric distance matrix which i created usign ClustalOmega program.

and used this R codes for clustering purpose.

*data=read.table("my_distance_matrix", header=FALSE)[-1]*
*attach(data)*
*head(data)*
*d=as.dist(data);*

*hc.complete=hclust(d,method="complete")*

*cutree(hc.complete, k=6)*
*groups<- cutree(hc.complete, k=6)*
*x<-cbind(groups)*
*x*
*x1<- subset(x,groups==1)*
*write.table(x, "results.txt", sep="\t")*
*plot(hc.complete)*


I am wondering am i doing wrong usign this code
?(*data=read.table("my_distance_matrix
or data file ???", header=FALSE)[-1]*)
Is this line requires normal data values?  In this line what kind of file
have to use? Normal data file or distance matrix?

*d=as.dist(data);      *With this line am i calculating twice distance
matrix?

Thanks in advance.
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d1dlwa_ 0.000000 0.655172 0.836207 0.827586 0.724138 0.896552 0.836207 0.870690 0.870690 0.896552
d2gkma_ 0.655172 0.000000 0.849206 0.803150 0.723577 0.874016 0.874016 0.881890 0.874016 0.858268
d2qrwa_ 0.836207 0.849206 0.000000 0.674603 0.804878 0.888889 0.865079 0.880952 0.896825 0.880952
d2bkma_ 0.827586 0.803150 0.674603 0.000000 0.804878 0.882812 0.890625 0.875000 0.882812 0.843750
d4i0va_ 0.724138 0.723577 0.804878 0.804878 0.000000 0.861789 0.829268 0.861789 0.886179 0.869919
d1asha_ 0.896552 0.874016 0.888889 0.882812 0.861789 0.000000 0.884354 0.890511 0.897059 0.871429
d2dc3a_ 0.836207 0.874016 0.865079 0.890625 0.829268 0.884354 0.000000 0.875912 0.845588 0.864286
d4hsxa_ 0.870690 0.881890 0.880952 0.875000 0.861789 0.890511 0.875912 0.000000 0.867647 0.883212
1ecaa_ 0.870690 0.874016 0.896825 0.882812 0.886179 0.897059 0.845588 0.867647 0.000000 0.882353
d1x9fd_ 0.896552 0.858268 0.880952 0.843750 0.869919 0.871429 0.864286 0.883212 0.882353 0.000000