I am attempting to create a tree for using with the R package MiRKAT, but as the documentation is very hard to understand, I hope someone in here can help me out.
My data is in the structure:
Acaryochloris Achromobacter Acidiphilium Acidisphaera
Sample1 23 1 0 4
Sample2 0 0 2 0
Sample3 4 0 4 0
Sample4 0 30 0 5
Sample5 11 0 5 0
Sample6 0 0 0 0
And the package takes a tree of the structure in the vignette:
List of 4
$ edge : int [1:1710, 1:2] 857 858 859 860 861 862 863 864 865 866 ...
$ Nnode : int 855
$ tip.label : chr [1:856] "1883" "3114" "1483" "2576" ...
$ edge.length: num [1:1710] 0.00846 0.09451 0.01012 0.01208 0.03501 ...
- attr(*, "class")= chr "phylo"
The vignette can be found on: http://research.fhcrc.org/content/dam/stripe/wu/files/MiRKAT/MiRKAT_Vignette.pdf
Is there any way to transform my data into such a tree structure? If so can you recommend any packages?
Sorry guys, I found out myself.
mydata_dist <- dist(mydata)
mydata_hc <- hclust(mydata_dist)
mydata_phyl <- as.phylo(mydata_hc)