Virtual Inference of Protein-activity by Enriched Regulon analysis


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Documentation for package ‘viper’ version 1.0.0

Help Pages

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