parameters {pbcmc} | R Documentation

## Accessors for MolecularPermutationClassifier child class slots

### Description

Slot setters/getters for MolecularPermutationClassifier hierarchy classes

### Usage

    parameters(object)

    ## S4 method for signature 'MolecularPermutationClassifier'
    parameters(object)

    parameters(object) <- value

    ## S4 replacement method for signature 'MolecularPermutationClassifier'
    parameters(object) <- value

    ## S4 method for signature 'MolecularPermutationClassifier'
    exprs(object)

    ## S4 replacement method for signature 'MolecularPermutationClassifier,ANY'
    exprs(object) <- value

    ## S4 method for signature 'MolecularPermutationClassifier'
    annotation(object, ...)

    ## S4 replacement method for signature 'MolecularPermutationClassifier,ANY'
    annotation(object) <- value

    targets(object)

    ## S4 method for signature 'MolecularPermutationClassifier'
    targets(object)

    targets(object) <- value

    ## S4 replacement method for signature 'MolecularPermutationClassifier'
    targets(object) <- value

    classification(object)

    ## S4 method for signature 'MolecularPermutationClassifier'
    classification(object)

    permutation(object)

    ## S4 method for signature 'MolecularPermutationClassifier'
    permutation(object)

### Arguments

`object` | MolecularPermutationClassifier subclass object
`value` | according to the function call: parameters: named list with at least the following fields: $nPerm integer with number of permutations. Default: 1e4L $where character with significant value used. Default value is "fdr". $pCutoff numeric with p-value or fdr cutoff used, i.e., variable<pCutoff. Default: 0.01 $corCutoff numeric with correlation difference between classes cutoff used, i.e., |ρ(profile,class_A)-ρ(profile,class_B)|>corCutoff $keep should null distribution simulation values be kept?. Default: FALSE annotation: data.frame with individual annotations (genes, etc). Minimal compulsory fields are: $probe same characters as in row.names(M). $EntrezGene.ID integer with NCBI Entrez Data Base. $NCBI.gene.symbol character with gene mnemonic, a.k.a. gene symbol. exprs: matrix with gene exprs profile, where genes are in rows and subjects as columns, a.k.a., M matrix. targets: data.frame with additional subject data.
`...` | additional parameters according to function call.

### Value

according to function call one of the following objects:

`parameters` | named list see value parameter
`exprs` | matrix with gene exprs profile, where genes are in rows and subjects as columns, a.k.a., M matrix.
`annotation` | data.frame see value parameter
`classification` | named list with at least the following fields:

$class

  factor with with all possible class levels.

`permutation` | named list with at least the following fields:

pvalues

  numeric matrix with subjects in row and classes in columns.

$fdr

  numeric matrix with False Discovery Rate correction of pvalues by row.

`parameters<-` | MolecularPermutationClassifier object with parameters updated slot.
`exprs<-` | MolecularPermutationClassifier object with exprs updated slot.
`annotation<-` | MolecularPermutationClassifier object with annotation updated slot.
`targets<-` | MolecularPermutationClassifier object with targets updated slot.

### Author(s)

Cristobal Fresno cfresno@bdmg.com.ar, German A. Gonzalez ggonzalez@bdmg.com.ar, Andrea S. Llera allera@leloir.org.ar and Elmer Andres Fernandez efernandez@bdmg.com.ar

### See Also

`PAM50` for a complete example.

Other MolecularPermutationClassifier: `MolecularPermutationClassifier-class`, `show`

### Examples

    ##Using pam50centroids package example data
    data(pam50centroids)

    ##Now we can inspect pam50centroids object
    head(exprs(pam50centroids))      ##The gene expression
    head(annotation(pam50centroids)) ##The available annotation
    head(targets(pam50centroids))    ##The clinical data present in the package

    ##Work with the parameters
    parameters(pam50centroids)       ##Display them
    aux<-parameters(pam50centroids)
    aux$keep<-TRUE                   ##Set keep to FALSE
    parameters(pam50centroids)<-aux
    parameters(pam50centroids)

    ##Also exprs<-, annotation<- and targets<- available functions to update
    ##the respective slots

[Package pbcmc version 1.8.0 Index]