[R] Hierarchical Clustering in R

[K. Elo]

Hi,

what is the exact problem? I tried you code and it works fine...

Best,
Kimmo

24.08.2016, 10:07, Serpil ŞEN wrote:
> 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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