create_rooted_tree: Create rooted tree from a taxonomy matrix
In trvinh/test: PhyloProfile

Description Usage Arguments Value Author(s) See Also Examples

Create rooted tree from a taxonomy matrix

1	create_rooted_tree(df, root_taxon)

`df`	data frame contains taxonomy matrix used for creating tree
`root_taxon`	taxon used for rooting tree

rooted tree based on root_taxon

Vinh Tran tran@bio.uni-frankfurt.de

taxa2dist for distance matrix generation from a taxonomy matrix, get_taxonomy_matrix for getting taxonomy matrix, pp_taxonomy_matrix for a demo taxonomy matrix data

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