phylogeneticCorrelations: Phylogenetic COmparative Method using LIMMA

In pbastide/phylolimma: Phylogenetic Comparative Methods for limma

Phylogenetic COmparative Method using LIMMA

Description

This function applies lmFit to the normalized data, in order to take the phylogeny into account. TODO: explain more.

Usage

phylogeneticCorrelations(
  object,
  design = NULL,
  phy,
  col_species = NULL,
  model = c("BM", "lambda", "OUfixedRoot", "OUrandomRoot", "delta"),
  measurement_error = TRUE,
  trim = 0.15,
  weights = NULL,
  REML = TRUE,
  ddf_method = c("Satterthwaite", "Species", "Samples"),
  ncores = 1,
  ...
)

Arguments

object	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'.
col_species	a character vector with same length as columns in the expression matrix, specifying the species for the corresponding column. If left 'NULL', an automatic parsing of species names with sample ids is attempted.
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.
trim	the fraction of observations to be trimmed from each end when computing the trimmed mean. Default to 0.15, as in duplicateCorrelation.
weights	a named vector or matrix with weights to be applied on the measurement error term. 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.
ncores	number of cores to use for parallel computation. Default to 1 (no parallel computation).
...	further parameters to be passed to lmFit.

Value

An object of class TransTree-class, with list components:

• tree the transformed consensus tree

• params the associated consensus parameters.

This consensus tree defines a correlation structure, and can be passed on to lmFit.

See Also

lmFit, phylolm, duplicateCorrelation

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