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 |
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