PIGShift (version 1.0.1)

test.groups: Test all possible single-rate shift Brownian motion models and an Ornstein-Uhlenbeck model for an arbitrary number of predefined gene groups.

Description

This function will find the maximum likelihood estimate of the parameters of every single rate shift model that is compatible with the phylogeny phy, as well as the likelihood and wAIC for each model and for each gene group. The procedure is described in Schraiber et al (2013).

Usage

test.groups(phy, dat, groups, norm = 1, print_names = F)

Arguments

phy

an ape format phylogeny

dat

a matrix of gene expression data. Rows of dat correspond to species and columns of dat correspond to genes

groups

a list of gene groups, formatted like the output of read.groups

norm

the species by which data should be normalized

print_names

a logical indicating whether to print the name of the group currently being analyzed. Useful to keep track of the progress of the function

Value

A list of several elements. wAIC is a matrix of Akaike weights for each model for each group (rows are groups, columns are models), alpha is the maximum likelihood shape parameter of the inverse gamma distribution for each model and group, beta is the maximum likelihood scale parameter of the inverse gamma distribution for each model and group, and shift is the maximum likelihood rate shift parameter for each model and each group, except for the final model which is Ornstein-Uhlenbeck, in which case it corresponds to the constraint parameter. Branches indicates which branches of the tree experience a rate shift.

Examples

## Not run: 
# data(yeast)
# GO.groups.pruned = good.groups(colnames(yeast.homozygote),GO.groups,30)
# to_test = GO.groups[GO.groups.pruned[1:100]]
# yeast.test = test.groups(yeast.tree,yeast.homozygote,to_test,print_names=T)
# ## End(Not run)