CytoK-class {cytoKernel} | R Documentation

## the CytoK class

### Description

Objects of this class store needed information to work with a CytoK object

### Value

`CytoKFeatures` returns the data.frame with shrunk effect size, shrunk effect size sd, unadjusted p value and adjusted p value for each feature, `CytoKFeaturesOrdered` returns the data.frame with shrunk effect size, shrunk effect size sd, unadjusted p value and adjusted p value for each feature ordered by unadjusted p value from low to high, `CytoKDEfeatures` returns the percent of differentially expressed features based on alpha (level of significance), `CytoKData` returns the original data object, `CytoKalpha` returns the specified level of significance. Default is alpha=0.05. `CytoKFeatureVars` returns the value of featureVars. Default is NULL.

### Slots

`CytoKFeatures`

  CytoK features

`CytoKFeaturesOrdered`

  CytoK features ordered by adjusted p values

`CytoKDEfeatures`

  Percent of Differentially Expressed CytoK features

`CytoKData`

  Original data object passed to `CytoK`

`CytoKalpha`

  Value of `alpha` argument passed to `CytoK`

`CytoKFeatureVars`

  Value of `featureVars` passed to `CytoK`. NULL if `featureVars` is left blank

### Examples

    data <- cbind(matrix(rnorm(1200,mean=2, sd=1.5),
    nrow=200, ncol=6), matrix(rnorm(1200,mean=5, sd=1.9),
    nrow=200, ncol=6))
    data_CytoK <- CytoK(object=data,
    group_factor = rep(c(0,1), each=6), lowerRho=2,
    upperRho=12,gridRho=4,alpha = 0.05,
    featureVars = NULL)

[Package cytoKernel version 1.0.0 Index]