edge-package | Extraction of Differential Gene Expression |
apply_qvalue | Estimate the q-values for a given set of p-values |
apply_qvalue-method | Estimate the q-values for a given set of p-values |
apply_snm | Supervised normalization of data in edge |
apply_snm-method | Supervised normalization of data in edge |
apply_sva | Estimate surrogate variables |
apply_sva-method | Estimate surrogate variables |
betaCoef | Regression coefficients from full model fit |
betaCoef-method | Regression coefficients from full model fit |
build_models | Generate a deSet object with full and null models |
build_study | Formulates the experimental models |
deFit-class | The differential expression class for the model fits |
deSet | Create a deSet object from an ExpressionSet |
deSet-class | The differential expression class (deSet) |
deSet-method | Create a deSet object from an ExpressionSet |
edge | Extraction of Differential Gene Expression |
endotoxin | Gene expression dataset from Calvano et al. (2005) Nature |
fitFull | Fitted data from the full model |
fitFull-method | Fitted data from the full model |
fitNull | Fitted data from the null model |
fitNull-method | Fitted data from the null model |
fit_models | Linear regression of the null and full models |
fit_models-method | Linear regression of the null and full models |
fullMatrix | Matrix representation of full model |
fullMatrix-method | Matrix representation of full model |
fullMatrix<- | Matrix representation of full model |
fullMatrix<--method | Matrix representation of full model |
fullModel | Full model equation |
fullModel-method | Full model equation |
fullModel<- | Full model equation |
fullModel<--method | Full model equation |
gibson | Gene expression dataset from Idaghdour et al. (2008) |
individual | Individuals sampled in experiment |
individual-method | Individuals sampled in experiment |
individual<- | Individuals sampled in experiment |
individual<--method | Individuals sampled in experiment |
kidney | Gene expression dataset from Rodwell et al. (2004) |
kl_clust | Modular optimal discovery procedure (mODP) |
kl_clust-method | Modular optimal discovery procedure (mODP) |
lrt | Performs F-test (likelihood ratio test using Normal likelihood) |
lrt-method | Performs F-test (likelihood ratio test using Normal likelihood) |
nullMatrix | Matrix representation of null model |
nullMatrix-method | Matrix representation of null model |
nullMatrix<- | Matrix representation of null model |
nullMatrix<--method | Matrix representation of null model |
nullModel | Null model equation from deSet object |
nullModel-method | Null model equation from deSet object |
nullModel<- | Null model equation from deSet object |
nullModel<--method | Null model equation from deSet object |
odp | The optimal discovery procedure |
odp-method | The optimal discovery procedure |
qvalueObj | Access/set qvalue slot |
qvalueObj-method | Access/set qvalue slot |
qvalueObj<- | Access/set qvalue slot |
qvalueObj<--method | Access/set qvalue slot |
resFull | Residuals of full model fit |
resFull-method | Residuals of full model fit |
resNull | Residuals of null model fit |
resNull-method | Residuals of null model fit |
show | Show function for deFit and deSet |
show-method | Show function for deFit and deSet |
sType | Statistic type used in analysis |
sType-method | Statistic type used in analysis |
summary | Summary of deFit and deSet |
summary-method | Summary of deFit and deSet |