ScudoResults-class {rScudo} | R Documentation |
This is an S4 class that represents the output of the functions
scudoTrain
and scudoTest
.
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).
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
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.
Matteo Ciciani matteo.ciciani@gmail.com, Thomas Cantore cantorethomas@gmail.com
# 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)