ScudoResults-class: Class ScudoResults

In Matteo-Ciciani/scudo: Signature-based Clustering for Diagnostic Purposes

Class ScudoResults

Description

This is an S4 class that represents the output of the functions scudoTrain and scudoTest.

Details

This class provides a structure to represent the results of scudoTrain and scudoTest. It contains the distance matrix and the gene signatures generated by the SCUDO analysis. It is possible, although not recommended, to manually create instances of this class (see Examples below).

Slots

distMatrix

a symmetric matrix with non-negative numeric elements

upSignatures

a data.frame with the same colnames as distMatrix, representing the up-regualted features in each sample

downSignatures

a data.frame with the same colnames as distMatrix, representing the down-regualted features in each sample

groupsAnnotation

a factor that represents the groups used for the computeFC and the feature selection

consensusUpSignatures

a data.frame that contains the consensus signatures of up-regulated features for each group

consensusDownSignatures

a data.frame that contains the consensus signatures of dowm-regulated features for each group

selectedFeatures

a character vector of selected features. If the feature selection was not performed, it contains every feature present in the input of the scudo functions

scudoParams

a list of the parameters used to run the function that created the instance of the class

Methods

distMatrix

signature(object = "ScudoResults"): a method for obtaining the distance matrix.

upSignatures

signature(object = "ScudoResults"): a method for obtaining the signature of up-regualted features in each sample.

downSignatures

signature(object = "ScudoResults"): a method for obtaining the signature of down-regulated features in each sample.

groupsAnnotation

signature(object = "ScudoResults"): a method for obtaining the groups used for computeFC and feature selection.

consensusUpSignatures

signature(object = "ScudoResults"): a method for obtaining the consensus signatures of up-regualted features in each group.

consensusDownSignatures

signature(object = "ScudoResults"): a method for obtaining the consensus signatures of down-regulated features in each group.

selectedFeatures

signature(object = "ScudoResults"): a method for obtaining the names of the features seleted. If no feature selection was performed, the names of every feature are returned.

scudoParams

signature(object = "ScudoResults"): a method for obtaining the parameters that were used to generate the result.

Author(s)

Matteo Ciciani [e-mail], Thomas Cantore [e-mail]

Examples

# manually generate instance of ScudoResults class
m <- matrix(1, ncol = 4, nrow = 4)
diag(m) <- 0
rownames(m) <- colnames(m) <- letters[1:4]
SigUp <- data.frame(a = letters[1:5], b = letters[6:10], c = letters[11:15],
    d = letters[16:20], stringsAsFactors = FALSE)
SigDown <- data.frame(a = letters[1:10], b = letters[11:20],
    c = letters[1:10], d = letters[11:20],
    stringsAsFactors = FALSE)
groups <- as.factor(c("G1", "G1", "G2", "G2"))
ConsUp <- data.frame(G1 = letters[11:15], G2 = letters[21:25],
    stringsAsFactors = FALSE)
ConsDown <- data.frame(G1 = letters[16:25], G2 = letters[1:10],
    stringsAsFactors = FALSE)
Feats <- letters[1:20]
Pars <- list()

scudoR <- ScudoResults(distMatrix = m,
    upSignatures = SigUp,
    downSignatures = SigDown,
    groupsAnnotation = groups,
    consensusUpSignatures = ConsUp,
    consensusDownSignatures = ConsDown,
    selectedFeatures = Feats,
    scudoParams = Pars)

Matteo-Ciciani/scudo documentation built on Feb. 3, 2024, 9:41 a.m.