createRootedTree: Create rooted tree from a taxonomy matrix
In PhyloProfile: PhyloProfile

Description Usage Arguments Value Author(s) See Also Examples

Create rooted tree from a taxonomy matrix

1	createRootedTree(df, rootTaxon = NULL)

`df`	data frame contains taxonomy matrix used for generating tree (see distDf in example)
`rootTaxon`	taxon used for rooting the taxonomy tree

A rooted taxonomy tree as an object of class "phylo".

Vinh Tran tran@bio.uni-frankfurt.de

taxa2dist for distance matrix generation from a taxonomy matrix, getTaxonomyMatrix for getting taxonomy matrix, ppTaxonomyMatrix for a demo taxonomy matrix data

data("ppTaxonomyMatrix", package = "PhyloProfile")
# prepare matrix for calculating distances
distDf <- subset(ppTaxonomyMatrix, select = -c(ncbiID, fullName))
row.names(distDf) <- distDf$abbrName
distDf <- distDf[, -1]
# create taxonomy tree rooted by ncbi10090
createRootedTree(distDf, "ncbi10090")