Polygenic Inverse Gamma Shifts

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Documentation for package ‘PIGShift’ version 1.0.1

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compute.sqrt.dist Compute the vector of branch scaling parameters
dmvnorminvgamma Compute the pdf for multi-variate normal-inverse-gamma random variates
dnorminvgamma Compute the pdf for normal-inverse-gamma random variates
GO.groups GO terms and genes
good.groups Find groups represented in the data
mean_invgamma The mean of the inverse gamma distribution
normalize.vcv Compute the variance-covariance matrix of normalized phylogenetic data
norminvgamma.shift.like.norm Calculate the likelihood of normalized comparative data as Brownian motions with inverse gamma distributed rates
norminvgamma.shift.sim.group Simulate phylogenetic comparative data as Brownian motions with inverse gamma distributed rates
OU.invgamma.like.norm Calculate the likelihood of normalized comparative data as OUs with inverse gamma distributed rates
OU.invgamma.sim.group Simulate phylogenetic comparative data as OUs with inverse gamma distributed rates
OU.vcv The variance covariance matrix for an Ornstein-Uhlenbeck process
plot_logfoldchange Plot densities of expression differences, possibly normalized
plot_wAICbarplot Plot a barplot of AIC weights for each model and each gene group
read.exp Read gene expression data from a file, sorted by a phylogenetic tree
read.groups Read in the members of a gene group
remove.from.genome Remove genes from a specified group from the data
rnorminvgamma Draw normal-inverse-gamma distributed random variates
test.groups Test all possible single-rate shift Brownian motion models and an Ornstein-Uhlenbeck model for an arbitrary number of predefined gene groups.
test.subtrees Test all possible single-rate shift Brownian motion models and an Ornstein-Uhlenbeck model
var_invgamma The variance of the inverse gamma distribution
yeast.homozygote Yeast homozygote transcription profiles
yeast.hybrid Yeast hybrid transcription profiles
yeast.tree Phylogenetic tree of yeast species