A bioconductor package for high-dimensional exploration of
biological network heterogeneity
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Documentation for package ‘nethet’ version 1.37.0
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. |
| 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' |