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

## Documentation for package ‘nethet’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'