Man pages for FrankD/nethet
A bioconductor package for high-dimensional exploration of biological network heterogeneity
| 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_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 |
