phyloCompData-class: Class phyloCompData

In csoneson/compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Class phyloCompData

Description

The phyloCompData class extends the compData class with sequence length and phylogeny related information.

Slots

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.

Methods

phylo.tree

signature(x="phyloCompData")

phylo.tree<-

signature(x="phyloCompData",value="phylo"): Get or set the tree in a phyloCompData object. value should be a phylo object.

length.matrix

signature(x="phyloCompData")

length.matrix<-

signature(x="phyloCompData",value="matrix"): Get or set the length matrix in a phyloCompData object. value should be a numeric matrix.

Construction

An object of the class phyloCompData can be constructed using the phyloCompData function.

Author(s)

Charlotte Soneson, Paul Bastide

csoneson/compcodeR documentation built on Oct. 25, 2023, 1:28 a.m.