PIGShift: Polygenic Inverse Gamma Shifts

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

Author
Joshua G. Schraiber <schraib@uw.edu>
Date of publication
2015-12-07 23:15:42
Maintainer
Joshua G. Schraiber <schraib@uw.edu>
License
GPL-3
Version
1.0.1

View on CRAN

Man pages

compute.sqrt.dist
Compute the vector of branch scaling parameters
dmvnorminvgamma
Compute the pdf for multi-variate normal-inverse-gamma random...
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...
norminvgamma.shift.like.norm
Calculate the likelihood of normalized comparative data as...
norminvgamma.shift.sim.group
Simulate phylogenetic comparative data as Brownian motions...
OU.invgamma.like.norm
Calculate the likelihood of normalized comparative data as...
OU.invgamma.sim.group
Simulate phylogenetic comparative data as OUs with inverse...
OU.vcv
The variance covariance matrix for an Ornstein-Uhlenbeck...
plot_logfoldchange
Plot densities of expression differences, possibly normalized
plot_wAICbarplot
Plot a barplot of AIC weights for each model and each gene...
read.exp
Read gene expression data from a file, sorted by a...
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...
test.subtrees
Test all possible single-rate shift Brownian motion models...
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

Files in this package

PIGShift
PIGShift/inst
PIGShift/inst/CITATION
PIGShift/NAMESPACE
PIGShift/data
PIGShift/data/yeast.rda
PIGShift/R
PIGShift/R/brownian_motion_package.r
PIGShift/MD5
PIGShift/DESCRIPTION
PIGShift/man
PIGShift/man/dmvnorminvgamma.Rd
PIGShift/man/normalize.vcv.Rd
PIGShift/man/yeast.homozygote.Rd
PIGShift/man/mean_invgamma.Rd
PIGShift/man/good.groups.Rd
PIGShift/man/OU.invgamma.like.norm.Rd
PIGShift/man/compute.sqrt.dist.Rd
PIGShift/man/read.groups.Rd
PIGShift/man/norminvgamma.shift.like.norm.Rd
PIGShift/man/GO.groups.Rd
PIGShift/man/OU.invgamma.sim.group.Rd
PIGShift/man/rnorminvgamma.Rd
PIGShift/man/plot_logfoldchange.Rd
PIGShift/man/test.groups.Rd
PIGShift/man/test.subtrees.Rd
PIGShift/man/plot_wAICbarplot.Rd
PIGShift/man/OU.vcv.Rd
PIGShift/man/dnorminvgamma.Rd
PIGShift/man/read.exp.Rd
PIGShift/man/var_invgamma.Rd
PIGShift/man/norminvgamma.shift.sim.group.Rd
PIGShift/man/remove.from.genome.Rd
PIGShift/man/yeast.tree.Rd
PIGShift/man/yeast.hybrid.Rd