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Phylogenetic correlation using a consensus tree

phylogeneticCorrelations.Rd

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"),
  measurement_error = TRUE,
  trim = c(0.25, 0.05),
  REML = TRUE,
  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" or "OUfixedRoot". 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

a vector of size two, with the fraction of observations to be trimmed from the lower and upper ends of `atanh(all.lambdas)` and `atanh(rho)` when computing the trimmed mean. If a single value is provided, it is recycled as a vector of size two. Default to `c(0.25, 0.05)`. See also the `trim` argument in duplicateCorrelation.

REML

Use REML (default) or ML for estimating the parameters.

ncores

number of cores to use for parallel computation. Default to 1 (no parallel computation).

...

further parameters to be passed to phylolm.

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

lmFit, phylolmFit, phylolm, eBayes