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

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).

AuthorNicolas Staedler, Frank Dondelinger
Date of publicationNone
MaintainerNicolas Staedler <staedler.n@gmail.com>, Frank Dondelinger <fdondelinger.work@gmail.com>
LicenseGPL-2
Version1.6.0

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

Functions

aggpval Man page
agg.pval Man page
agg.score.iriz.scale Man page
agg.score.iriz.shift Man page
aic.glasso Man page
beta.mat Man page
beta.mat.diffregr Man page
bic.glasso Man page
buildDotPlotDataFrame Man page
bwprun_mixglasso Man page
cv.fold Man page
cv.glasso Man page
diffnet_multisplit Man page
diffnet_pval Man page
diffnet_singlesplit Man page
diffregr_multisplit Man page
diffregr_pval Man page
diffregr_singlesplit Man page
dot_plot Man page
error.bars Man page
est2.my.ev2 Man page
est2.my.ev2.diffregr Man page
est2.my.ev3 Man page
est2.my.ev3.diffregr Man page
est2.ww.mat2 Man page
est2.ww.mat2.diffregr Man page
est2.ww.mat.diffregr Man page
export_network Man page
EXPStep.mix Man page
func.uinit Man page
generate_2networks Man page
generate_inv_cov Man page
getinvcov Man page
ggmgsa_multisplit Man page
ggmgsa_singlesplit Man page
glasso.invcor Man page
glasso.invcov Man page
glasso.parcor Man page
gsea.highdimT2 Man page
gsea.iriz Man page
gsea.iriz.scale Man page
gsea.iriz.shift Man page
gsea.t2cov Man page
het_cv_glasso Man page
hugepath Man page
inf.mat Man page
invcov2parcor Man page
invcov2parcor_array Man page
lambdagrid_lin Man page
lambdagrid_mult Man page
lambda.max Man page
loglik_mix Man page
logratio Man page
logratio.diffregr Man page
make_grid Man page
mcov Man page
mixglasso Man page
mixglasso_init Man page
mixglasso_ncomp_fixed Man page
mle.ggm Man page
MStepGlasso Man page
my.ev2.diffregr Man page
my.p.adjust Man page
mytrunc.method Man page
my.ttest Man page
my.ttest2 Man page
NetHet-package Man page
perm.diffregr_pval Man page
perm.diffregr_teststat Man page
plot_2networks Man page
plotCV Man page
plot.diffnet Man page
plot.diffregr Man page
plot.ggmgsa Man page
plot.nethetclustering Man page
print.nethetsummary Man page
q.matrix3 Man page
q.matrix4 Man page
q.matrix.diffregr Man page
q.matrix.diffregr3 Man page
q.matrix.diffregr4 Man page
scatter_plot Man page
screen_aic.glasso Man page
screen_bic.glasso Man page
screen_cv1se.lasso Man page
screen_cvfix.lasso Man page
screen_cv.glasso Man page
screen_cvmin.lasso Man page
screen_cvsqrt.lasso Man page
screen_cvtrunc.lasso Man page
screen_full Man page
screen_lasso Man page
screen_mb Man page
screen_mb2 Man page
screen_shrink Man page
shapiro_screen Man page
sim_mix Man page
sim_mix_networks Man page
sparse_conc Man page
summary.diffnet Man page
summary.diffregr Man page
summary.ggmgsa Man page
summary.nethetclustering Man page
sumoffdiag Man page
symmkldist Man page
t2cov.lr Man page
t2diagcov.lr Man page
test.sd Man page
test.t2 Man page
tr Man page
twosample_single_regr Man page
w.kldist Man page
ww.mat Man page
ww.mat2 Man page
ww.mat2.diffregr Man page
ww.mat.diffregr Man page

Files

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

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