createRootedTree {PhyloProfile} | R Documentation |
Create rooted tree from a taxonomy matrix
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")