PIGShift: Polygenic Inverse Gamma Shifts

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

Install the latest version of this package by entering the following in R:
install.packages("PIGShift")
AuthorJoshua G. Schraiber <schraib@uw.edu>
Date of publication2015-12-07 23:15:42
MaintainerJoshua G. Schraiber <schraib@uw.edu>
LicenseGPL-3
Version1.0.1

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

Functions

compute.sqrt.dist Man page
dmvnorminvgamma Man page
dnorminvgamma Man page
GO.groups Man page
good.groups Man page
mean_invgamma Man page
normalize.vcv Man page
norminvgamma.shift.like.norm Man page
norminvgamma.shift.sim.group Man page
OU.invgamma.like.norm Man page
OU.invgamma.sim.group Man page
OU.vcv Man page
plot_logfoldchange Man page
plot_wAICbarplot Man page
read.exp Man page
read.groups Man page
remove.from.genome Man page
rnorminvgamma Man page
test.groups Man page
test.subtrees Man page
var_invgamma Man page
yeast.homozygote Man page
yeast.hybrid Man page
yeast.tree Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.