Learn R Programming

PIGShift (version 1.0.1)

Polygenic Inverse Gamma Shifts

Description

Fits models of gene expression evolution to expression data from coregulated groups of genes, assuming inverse gamma distributed rate variation.

Copy Link

Version

Install

install.packages('PIGShift')

Monthly Downloads

15

Version

1.0.1

License

GPL-3

Maintainer

Joshua G Schraiber

Last Published

December 7th, 2015

Functions in PIGShift (1.0.1)

dmvnorminvgamma

Compute the pdf for multi-variate normal-inverse-gamma random variates
good.groups

Find groups represented in the data
normalize.vcv

Compute the variance-covariance matrix of normalized phylogenetic data
norminvgamma.shift.sim.group

Simulate phylogenetic comparative data as Brownian motions with inverse gamma distributed rates
norminvgamma.shift.like.norm

Calculate the likelihood of normalized comparative data as Brownian motions with inverse gamma distributed rates
dnorminvgamma

Compute the pdf for normal-inverse-gamma random variates
compute.sqrt.dist

Compute the vector of branch scaling parameters
OU.invgamma.like.norm

Calculate the likelihood of normalized comparative data as OUs with inverse gamma distributed rates
GO.groups

GO terms and genes
mean_invgamma

The mean of the inverse gamma distribution
OU.vcv

The variance covariance matrix for an Ornstein-Uhlenbeck process
test.subtrees

Test all possible single-rate shift Brownian motion models and an Ornstein-Uhlenbeck model
read.groups

Read in the members of a gene group
test.groups

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

Remove genes from a specified group from the data
rnorminvgamma

Draw normal-inverse-gamma distributed random variates
plot_logfoldchange

Plot densities of expression differences, possibly normalized
plot_wAICbarplot

Plot a barplot of AIC weights for each model and each gene group
OU.invgamma.sim.group

Simulate phylogenetic comparative data as OUs with inverse gamma distributed rates
read.exp

Read gene expression data from a file, sorted by a phylogenetic tree
var_invgamma

The variance of the inverse gamma distribution
yeast.tree

Phylogenetic tree of yeast species
yeast.hybrid

Yeast hybrid transcription profiles
yeast.homozygote

Yeast homozygote transcription profiles