The phyloCompData class extends the compData class
with sequence length and phylogeny related information.
tree:The phylogenetic tree describing the relationships between samples. The taxa names of the tree should be the same as the column names of the count.matrix. Class phylo.
length.matrix:The length matrix, with genes as rows and samples as columns. The column names of the length.matrix should be the same as the column names of the count.matrix. Class matrix.
sample.annotations:In addition to the columns described in the compData class, if the tree is specified, it should contain an extra column named id.species of factors giving the species for each sample. The row names should be the same as the column names of count.matrix. Class data.frame.
signature(x="phyloCompData")
signature(x="phyloCompData",value="phylo"):
Get or set the tree in a phyloCompData object. value should be a phylo object.
signature(x="phyloCompData")
signature(x="phyloCompData",value="matrix"):
Get or set the length matrix in a phyloCompData object. value should be a numeric matrix.
An object of the class phyloCompData can be constructed using the phyloCompData function.