aracne2regulon | Regulon object generation from ARACNe results |
as.dist.signatureDistance | Distance matrix from signatureDistance objects |
bootstrapmsviper | msviper bootstraps integration |
bootstrapTtest | Bootstrapped signature by t-test |
bootstrapTtest-method | Bootstrapped signature by t-test |
comNames | Combinatorial annotation |
distMode | Mode of continuous distributions |
fcvarna | Variance of columns for arrays with NA values |
filterColMatrix | Filter for columns of a matrix with no loss of col and row names |
filterCV | Coefficient of variation filter |
filterCV-method | Coefficient of variation filter |
filterRowMatrix | Filter for rows of a matrix with no loss of col and row names |
frcv | Coeficient of variations for rows |
frvarna | Variance of rows for arrays with NA values |
groupPwea3 | Proportionally Weighted Enrichment Analysis for gene-set groups |
integrateSignatures | Integrate signatures |
ledge | Leading-edge analysis |
loadExpset | Loading expression sets |
msviper | msVIPER |
msviper-class | The msviper class |
msviperAnnot | msVIPER annotation change |
msviperCombinatorial | msviper combinatorial analysis |
msviperSynergy | msviper synergy analysis |
plot.msviper | Plot msviper results |
pruneRegulon | Prune Regulons |
pwea3NULLf | Null model function |
pwea3NULLgroups | Regulon-specific NULL model |
regulon-class | The regulon class |
rowTtest | Student's t-test for rows |
rowTtest-method | Student's t-test for rows |
scale.signatureDistance | Scaling of signatureDistance objects |
scaleGroups | Signatures with grouping variable |
shadow | Shadow analysis for msviper objects |
signatureDistance | Signature Distance |
signatureDistance-class | signatureDistance |
summary.msviper | List msviper results |
ttestNull | Null model by sample permutation testing |
ttestNull-method | Null model by sample permutation testing |
viper | VIPER |
viperSignature | Generic S4 method for signature and sample-permutation null model for VIPER |
viperSignature-class | viperSignature |
viperSignature-method | Generic S4 method for signature and sample-permutation null model for VIPER |