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

aggpvalMeinshausen p-value aggregation
agg.pvalP-value aggregation (Meinshausen et al 2009)
agg.score.iriz.scaleIrizarry aggregate score (scale)
agg.score.iriz.shiftIrizarry aggregate score (shift)
aic.glassoAIC.glasso
beta.matCompute beta-matrix
beta.mat.diffregrComputation beta matrix
bic.glassoBIC.glasso
buildDotPlotDataFrameBuild up dataframe for plotting dot plot with ggplot2
bwprun_mixglassobwprun_mixglasso
cv.foldMake folds
cv.glassoCrossvalidation for GLasso
diffnet_multisplitDifferential Network
diffnet_pvalP-value calculation
diffnet_singlesplitDifferential Network for user specified data splits
diffregr_multisplitDifferential Regression (multi-split version).
diffregr_pvalComputation "split-asym" p-values.
diffregr_singlesplitDifferential Regression (single-split version).
dot_plotCreate a plot showing the edges with the highest partial...
error.barsError bars for plotCV
est2.my.ev2Weights of sum-w-chi2
est2.my.ev2.diffregrCompute weights of sum-w-chi2 (2nd order simplification)
est2.my.ev3Compute weights of sum-of-weighted-chi2s
est2.my.ev3.diffregrCompute weights of sum-of-weighted-chi2s
est2.ww.mat2Weights of sum-w-chi2
est2.ww.mat2.diffregrEstimate weights
est2.ww.mat.diffregrEstimate weights
export_networkExport networks as a CSV table.
EXPStep.mixPerforms EStep
func.uinitInitialization of MixGLasso
generate_2networksGenerate sparse invcov with overlap
generate_inv_covgenerate_inv_cov
getinvcovGenerate an inverse covariance matrix with a given sparsity...
ggmgsa_multisplitMulti-split GGMGSA (parallelized computation)
ggmgsa_singlesplitSingle-split GGMGSA
glasso.invcorGraphical Lasso based on inverse covariance penalty
glasso.invcovGraphical Lasso based on inverse correlation penalty
glasso.parcorGraphical Lasso based on partial correlation penalty
gsea.highdimT2GSA based on HighdimT2
gsea.irizIrizarry approach for gene-set testing
gsea.iriz.scaleIrizarry approach (scale only)
gsea.iriz.shiftIrizarry approach (shift only)
gsea.t2covGSA using T2cov-test
het_cv_glassoCross-validated glasso on heterogeneous dataset with grouping
hugepathGraphical Lasso path with huge package
inf.matInformation Matrix of Gaussian Graphical Model
invcov2parcorConvert inverse covariance to partial correlation
invcov2parcor_arrayConvert inverse covariance to partial correlation for several...
lambdagrid_linLambda-grid
lambdagrid_multLambda-grid
lambda.maxLambdamax
loglik_mixLog-likelihood for mixture model
logratioLog-likelihood-ratio statistics used in DiffNet
logratio.diffregrLog-likelihood ratio statistics for Differential Regression.
make_gridMake grid
mcovCompute covariance matrix
mixglassomixglasso
mixglasso_initmixglasso_init
mixglasso_ncomp_fixedmixglasso_ncomp_fixed
mle.ggmMLE in GGM
MStepGlassoMStep of MixGLasso
my.ev2.diffregrComputation eigenvalues
my.p.adjustP-value adjustment
mytrunc.methodAdditional thresholding
my.ttestT-test
my.ttest2T-test
NetHet-packageNetHet-package
perm.diffregr_pvalComputation "split-perm" p-value.
perm.diffregr_teststatAuxiliary function for computation of "split-perm" p-value.
plot_2networksPlot two networks (GGMs)
plotCVplotCV
plot.diffnetPlotting function for object of class 'diffnet'
plot.diffregrPlotting function for object of class 'diffregr'
plot.ggmgsaPlotting function for object of class 'ggmgmsa'
plot.nethetclusteringPlot networks
print.nethetsummaryPrint function for object of class 'nethetsummmary'
q.matrix3Compute Q-matrix
q.matrix4q.matrix4
q.matrix.diffregrComputation Q matrix
q.matrix.diffregr3Computation Q matrix
q.matrix.diffregr4Computation Q matrix
scatter_plotCreate a scatterplot showing correlation between specific...
screen_aic.glassoAIC-tuned glasso with additional thresholding
screen_bic.glassoBIC-tuned glasso with additional thresholding
screen_cv1se.lassoCross-validated Lasso screening (lambda.1se-rule)
screen_cvfix.lassoCross-validated Lasso screening and upper bound on number of...
screen_cv.glassoCross-validated glasso with additional thresholding
screen_cvmin.lassoCross-validation lasso screening (lambda.min-rule)
screen_cvsqrt.lassoCross-validated Lasso screening and sqrt-truncation.
screen_cvtrunc.lassoCross-validated Lasso screening and additional truncation.
screen_fullScreen_full
screen_lassoScreen_lasso
screen_mbNode-wise Lasso-regressions for GGM estimation
screen_mb2Screen_mb2
screen_shrinkShrinkage approach for estimating Gaussian graphical model
shapiro_screenFilter "non-normal" genes
sim_mixSimulate from mixture model.
sim_mix_networkssim_mix_networks
sparse_concGenerates sparse inverse covariance matrices
summary.diffnetSummary function for object of class 'diffnet'
summary.diffregrSummary function for object of class 'diffregr'
summary.ggmgsaSummary function for object of class 'ggmgsa'
summary.nethetclusteringSummary function for object of class 'nethetclustering'
sumoffdiagSum of non-diag elements of a matrix
symmkldistCompute symmetric kull-back leibler distance
t2cov.lrClassical likelihood-ratio test
t2diagcov.lrDiagonal-restricted likelihood-ratio test
test.sdHigh-Dim Two-Sample Test (Srivastava, 2006)
test.t2HotellingsT2
trCompute trace of matrix
twosample_single_regrold single-split function for diffregr
w.kldistDistance between comps based on symm. kl-distance
ww.matWeight-matrix and eigenvalues
ww.mat2Calculates eigenvalues of weight-matrix (using 1st order...
ww.mat2.diffregrComputation M matrix and eigenvalues
ww.mat.diffregrComputation M matrix and eigenvalues
nethet documentation built on Nov. 17, 2017, 12:04 p.m.