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


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Documentation for package ‘nethet’ version 1.4.2

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NetHet-package NetHet-package
aggpval Meinshausen p-value aggregation
bwprun_mixglasso bwprun_mixglasso
diffnet_multisplit Differential Network
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 correlation in any cluster.
export_network Export networks as a CSV table.
generate_2networks Generate sparse invcov with overlap
generate_inv_cov generate_inv_cov
ggmgsa_multisplit Multi-split GGMGSA (parallelized computation)
ggmgsa_singlesplit Single-split GGMGSA
gsea.iriz Irizarry approach for gene-set testing
het_cv_glasso Cross-validated glasso on heterogeneous dataset with grouping
invcov2parcor Convert inverse covariance to partial correlation
invcov2parcor_array Convert inverse covariance to partial correlation for several inverse covariance matrices collected in an array.
logratio Log-likelihood-ratio statistics used in DiffNet
mixglasso mixglasso
mixglasso_init mixglasso_init
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
plot_2networks Plot two networks (GGMs)
print.nethetsummary Print function for object of class 'nethetsummmary'
scatter_plot Create a scatterplot showing correlation between specific nodes in the network for each pre-specified group.
screen_aic.glasso AIC-tuned glasso with additional thresholding
screen_bic.glasso BIC-tuned glasso with additional thresholding
screen_cv.glasso Cross-validated 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 predictors.
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_mb Node-wise Lasso-regressions for GGM estimation
sim_mix Simulate from mixture model.
sim_mix_networks sim_mix_networks
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'