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.

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.