nethet: A bioconductor package for high-dimensional exploration of biological network heterogeneity

Share:

Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional data. It combines several implementations of recent statistical innovations useful for estimation and comparison of networks in a heterogeneous, high-dimensional setting. In particular, we provide code for formal two-sample testing in Gaussian graphical models (differential network and GGM-GSA; Stadler and Mukherjee, 2013, 2014) and make a novel network-based clustering algorithm available (mixed graphical lasso, Stadler and Mukherjee, 2013).

Author
Nicolas Staedler, Frank Dondelinger
Date of publication
None
Maintainer
Nicolas Staedler <staedler.n@gmail.com>, Frank Dondelinger <fdondelinger.work@gmail.com>
License
GPL-2
Version
1.6.0

View on Bioconductor

Man pages

aggpval
Meinshausen p-value aggregation
agg.pval
P-value aggregation (Meinshausen et al 2009)
agg.score.iriz.scale
Irizarry aggregate score (scale)
agg.score.iriz.shift
Irizarry aggregate score (shift)
aic.glasso
AIC.glasso
beta.mat
Compute beta-matrix
beta.mat.diffregr
Computation beta matrix
bic.glasso
BIC.glasso
buildDotPlotDataFrame
Build up dataframe for plotting dot plot with ggplot2
bwprun_mixglasso
bwprun_mixglasso
cv.fold
Make folds
cv.glasso
Crossvalidation for GLasso
diffnet_multisplit
Differential Network
diffnet_pval
P-value calculation
diffnet_singlesplit
Differential Network for user specified data splits
diffregr_multisplit
Differential Regression (multi-split version).
diffregr_pval
Computation "split-asym" p-values.
diffregr_singlesplit
Differential Regression (single-split version).
dot_plot
Create a plot showing the edges with the highest partial...
error.bars
Error bars for plotCV
est2.my.ev2
Weights of sum-w-chi2
est2.my.ev2.diffregr
Compute weights of sum-w-chi2 (2nd order simplification)
est2.my.ev3
Compute weights of sum-of-weighted-chi2s
est2.my.ev3.diffregr
Compute weights of sum-of-weighted-chi2s
est2.ww.mat2
Weights of sum-w-chi2
est2.ww.mat2.diffregr
Estimate weights
est2.ww.mat.diffregr
Estimate weights
export_network
Export networks as a CSV table.
EXPStep.mix
Performs EStep
func.uinit
Initialization of MixGLasso
generate_2networks
Generate sparse invcov with overlap
generate_inv_cov
generate_inv_cov
getinvcov
Generate an inverse covariance matrix with a given sparsity...
ggmgsa_multisplit
Multi-split GGMGSA (parallelized computation)
ggmgsa_singlesplit
Single-split GGMGSA
glasso.invcor
Graphical Lasso based on inverse covariance penalty
glasso.invcov
Graphical Lasso based on inverse correlation penalty
glasso.parcor
Graphical Lasso based on partial correlation penalty
gsea.highdimT2
GSA based on HighdimT2
gsea.iriz
Irizarry approach for gene-set testing
gsea.iriz.scale
Irizarry approach (scale only)
gsea.iriz.shift
Irizarry approach (shift only)
gsea.t2cov
GSA using T2cov-test
het_cv_glasso
Cross-validated glasso on heterogeneous dataset with grouping
hugepath
Graphical Lasso path with huge package
inf.mat
Information Matrix of Gaussian Graphical Model
invcov2parcor
Convert inverse covariance to partial correlation
invcov2parcor_array
Convert inverse covariance to partial correlation for several...
lambdagrid_lin
Lambda-grid
lambdagrid_mult
Lambda-grid
lambda.max
Lambdamax
loglik_mix
Log-likelihood for mixture model
logratio
Log-likelihood-ratio statistics used in DiffNet
logratio.diffregr
Log-likelihood ratio statistics for Differential Regression.
make_grid
Make grid
mcov
Compute covariance matrix
mixglasso
mixglasso
mixglasso_init
mixglasso_init
mixglasso_ncomp_fixed
mixglasso_ncomp_fixed
mle.ggm
MLE in GGM
MStepGlasso
MStep of MixGLasso
my.ev2.diffregr
Computation eigenvalues
my.p.adjust
P-value adjustment
mytrunc.method
Additional thresholding
my.ttest
T-test
my.ttest2
T-test
NetHet-package
NetHet-package
perm.diffregr_pval
Computation "split-perm" p-value.
perm.diffregr_teststat
Auxiliary function for computation of "split-perm" p-value.
plot_2networks
Plot two networks (GGMs)
plotCV
plotCV
plot.diffnet
Plotting function for object of class 'diffnet'
plot.diffregr
Plotting function for object of class 'diffregr'
plot.ggmgsa
Plotting function for object of class 'ggmgmsa'
plot.nethetclustering
Plot networks
print.nethetsummary
Print function for object of class 'nethetsummmary'
q.matrix3
Compute Q-matrix
q.matrix4
q.matrix4
q.matrix.diffregr
Computation Q matrix
q.matrix.diffregr3
Computation Q matrix
q.matrix.diffregr4
Computation Q matrix
scatter_plot
Create a scatterplot showing correlation between specific...
screen_aic.glasso
AIC-tuned glasso with additional thresholding
screen_bic.glasso
BIC-tuned glasso with additional thresholding
screen_cv1se.lasso
Cross-validated Lasso screening (lambda.1se-rule)
screen_cvfix.lasso
Cross-validated Lasso screening and upper bound on number of...
screen_cv.glasso
Cross-validated glasso with additional thresholding
screen_cvmin.lasso
Cross-validation lasso screening (lambda.min-rule)
screen_cvsqrt.lasso
Cross-validated Lasso screening and sqrt-truncation.
screen_cvtrunc.lasso
Cross-validated Lasso screening and additional truncation.
screen_full
Screen_full
screen_lasso
Screen_lasso
screen_mb
Node-wise Lasso-regressions for GGM estimation
screen_mb2
Screen_mb2
screen_shrink
Shrinkage approach for estimating Gaussian graphical model
shapiro_screen
Filter "non-normal" genes
sim_mix
Simulate from mixture model.
sim_mix_networks
sim_mix_networks
sparse_conc
Generates sparse inverse covariance matrices
summary.diffnet
Summary function for object of class 'diffnet'
summary.diffregr
Summary function for object of class 'diffregr'
summary.ggmgsa
Summary function for object of class 'ggmgsa'
summary.nethetclustering
Summary function for object of class 'nethetclustering'
sumoffdiag
Sum of non-diag elements of a matrix
symmkldist
Compute symmetric kull-back leibler distance
t2cov.lr
Classical likelihood-ratio test
t2diagcov.lr
Diagonal-restricted likelihood-ratio test
test.sd
High-Dim Two-Sample Test (Srivastava, 2006)
test.t2
HotellingsT2
tr
Compute trace of matrix
twosample_single_regr
old single-split function for diffregr
w.kldist
Distance between comps based on symm. kl-distance
ww.mat
Weight-matrix and eigenvalues
ww.mat2
Calculates eigenvalues of weight-matrix (using 1st order...
ww.mat2.diffregr
Computation M matrix and eigenvalues
ww.mat.diffregr
Computation M matrix and eigenvalues

Files in this package

nethet/DESCRIPTION
nethet/NAMESPACE
nethet/R
nethet/R/auxfunc.R
nethet/R/cvglasso.R
nethet/R/diffnet.R
nethet/R/diffregr.R
nethet/R/ggmgsa.R
nethet/R/mixglasso.R
nethet/R/nethet.R
nethet/R/netplot.R
nethet/R/netsim.R
nethet/README.md
nethet/build
nethet/build/vignette.rds
nethet/inst
nethet/inst/NEWS
nethet/inst/doc
nethet/inst/doc/nethet.R
nethet/inst/doc/nethet.Rnw
nethet/inst/doc/nethet.pdf
nethet/man
nethet/man/EXPStep.mix.Rd
nethet/man/MStepGlasso.Rd
nethet/man/NetHet-package.Rd
nethet/man/agg.pval.Rd
nethet/man/agg.score.iriz.scale.Rd
nethet/man/agg.score.iriz.shift.Rd
nethet/man/aggpval.Rd
nethet/man/aic.glasso.Rd
nethet/man/beta.mat.Rd
nethet/man/beta.mat.diffregr.Rd
nethet/man/bic.glasso.Rd
nethet/man/buildDotPlotDataFrame.Rd
nethet/man/bwprun_mixglasso.Rd
nethet/man/cv.fold.Rd
nethet/man/cv.glasso.Rd
nethet/man/diffnet_multisplit.Rd
nethet/man/diffnet_pval.Rd
nethet/man/diffnet_singlesplit.Rd
nethet/man/diffregr_multisplit.Rd
nethet/man/diffregr_pval.Rd
nethet/man/diffregr_singlesplit.Rd
nethet/man/dot_plot.Rd
nethet/man/error.bars.Rd
nethet/man/est2.my.ev2.Rd
nethet/man/est2.my.ev2.diffregr.Rd
nethet/man/est2.my.ev3.Rd
nethet/man/est2.my.ev3.diffregr.Rd
nethet/man/est2.ww.mat.diffregr.Rd
nethet/man/est2.ww.mat2.Rd
nethet/man/est2.ww.mat2.diffregr.Rd
nethet/man/export_network.Rd
nethet/man/func.uinit.Rd
nethet/man/generate_2networks.Rd
nethet/man/generate_inv_cov.Rd
nethet/man/getinvcov.Rd
nethet/man/ggmgsa_multisplit.Rd
nethet/man/ggmgsa_singlesplit.Rd
nethet/man/glasso.invcor.Rd
nethet/man/glasso.invcov.Rd
nethet/man/glasso.parcor.Rd
nethet/man/gsea.highdimT2.Rd
nethet/man/gsea.iriz.Rd
nethet/man/gsea.iriz.scale.Rd
nethet/man/gsea.iriz.shift.Rd
nethet/man/gsea.t2cov.Rd
nethet/man/het_cv_glasso.Rd
nethet/man/hugepath.Rd
nethet/man/inf.mat.Rd
nethet/man/invcov2parcor.Rd
nethet/man/invcov2parcor_array.Rd
nethet/man/lambda.max.Rd
nethet/man/lambdagrid_lin.Rd
nethet/man/lambdagrid_mult.Rd
nethet/man/loglik_mix.Rd
nethet/man/logratio.Rd
nethet/man/logratio.diffregr.Rd
nethet/man/make_grid.Rd
nethet/man/mcov.Rd
nethet/man/mixglasso.Rd
nethet/man/mixglasso_init.Rd
nethet/man/mixglasso_ncomp_fixed.Rd
nethet/man/mle.ggm.Rd
nethet/man/my.ev2.diffregr.Rd
nethet/man/my.p.adjust.Rd
nethet/man/my.ttest.Rd
nethet/man/my.ttest2.Rd
nethet/man/mytrunc.method.Rd
nethet/man/perm.diffregr_pval.Rd
nethet/man/perm.diffregr_teststat.Rd
nethet/man/plot.diffnet.Rd
nethet/man/plot.diffregr.Rd
nethet/man/plot.ggmgsa.Rd
nethet/man/plot.nethetclustering.Rd
nethet/man/plotCV.Rd
nethet/man/plot_2networks.Rd
nethet/man/print.nethetsummary.Rd
nethet/man/q.matrix.diffregr.Rd
nethet/man/q.matrix.diffregr3.Rd
nethet/man/q.matrix.diffregr4.Rd
nethet/man/q.matrix3.Rd
nethet/man/q.matrix4.Rd
nethet/man/scatter_plot.Rd
nethet/man/screen_aic.glasso.Rd
nethet/man/screen_bic.glasso.Rd
nethet/man/screen_cv.glasso.Rd
nethet/man/screen_cv1se.lasso.Rd
nethet/man/screen_cvfix.lasso.Rd
nethet/man/screen_cvmin.lasso.Rd
nethet/man/screen_cvsqrt.lasso.Rd
nethet/man/screen_cvtrunc.lasso.Rd
nethet/man/screen_full.Rd
nethet/man/screen_lasso.Rd
nethet/man/screen_mb.Rd
nethet/man/screen_mb2.Rd
nethet/man/screen_shrink.Rd
nethet/man/shapiro_screen.Rd
nethet/man/sim_mix.Rd
nethet/man/sim_mix_networks.Rd
nethet/man/sparse_conc.Rd
nethet/man/summary.diffnet.Rd
nethet/man/summary.diffregr.Rd
nethet/man/summary.ggmgsa.Rd
nethet/man/summary.nethetclustering.Rd
nethet/man/sumoffdiag.Rd
nethet/man/symmkldist.Rd
nethet/man/t2cov.lr.Rd
nethet/man/t2diagcov.lr.Rd
nethet/man/test.sd.Rd
nethet/man/test.t2.Rd
nethet/man/tr.Rd
nethet/man/twosample_single_regr.Rd
nethet/man/w.kldist.Rd
nethet/man/ww.mat.Rd
nethet/man/ww.mat.diffregr.Rd
nethet/man/ww.mat2.Rd
nethet/man/ww.mat2.diffregr.Rd
nethet/src
nethet/src/betamat_diffnet.c
nethet/tests
nethet/tests/Examples
nethet/tests/Examples/diffnet_ex.R
nethet/tests/Examples/diffnet_ss_ex.R
nethet/tests/Examples/diffregr_ex.R
nethet/tests/Examples/diffregr_ss_ex.R
nethet/tests/Examples/ggmgsa_ex.R
nethet/tests/Examples/mixglasso_ex.R
nethet/tests/testthat
nethet/tests/testthat/mixglasso_tests.r
nethet/tests/testthat/netsim_test.r
nethet/vignettes
nethet/vignettes/nethet.Rnw
nethet/vignettes/nethet.bib