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

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

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