get_chol_tree: Get Tree Normalizing Inverse Cholesky

In pbastide/phylolimma: Phylogenetic Comparative Methods for limma

Get Tree Normalizing Inverse Cholesky

Description

Compute the whitening cholesky matrix.

Usage

get_chol_tree(
  y_data,
  design,
  phy,
  phy_ind = NULL,
  model,
  measurement_error,
  REML,
  ddf_method,
  ...
)

Arguments

y_data	A matrix data object containing normalized expression values, with rows corresponding to genes and columns to samples (species).
design	the design matrix of the experiment, with rows corresponding to samples and columns to coefficients to be estimated. Defaults to the unit vector (intercept).
phy	an object of class phylo. It must be either a tree with tips having the same names as the columns of object (including replicates), or a tree such that tip labels match with species names in 'col_species'.
model	the phylogenetic model used to correct for the phylogeny. Must be one of "BM", "lambda", "OUfixedRoot", "OUrandomRoot" or "delta". See phylolm for more details.
measurement_error	a logical value indicating whether there is measurement error. Default to TRUE. See phylolm for more details.
REML	Use REML (default) or ML for estimating the parameters.
ddf_method	the method for the computation of the degrees of freedom of the t statistics (before moderation). Default to ddf_method="Satterthwaite". If ddf_method="Species", then the number of species is taken for the computation of the degrees of freedom, while if ddf_method="Samples" the total number of individuals is used.
...	further parameters to be passed to lmFit or phylolm.

Value

The (list of) cholesky matrix of the tree structure.

pbastide/phylolimma documentation built on Nov. 17, 2024, 1:34 p.m.