CytoKDEData {cytoKernel} | R Documentation

## Differentially expressed data by cytoKernel

### Description

Select `CytoK` object according to the differentially expressed features identified by cytoKernel. Features are filtered if their adjusted p values are greater than `CytoKalpha`.

### Usage

    CytoKDEData(object, by = c("features"))

### Arguments

`object` | a CytoK object from `CytoK`
`by` | String specifying which adjusted p values of the features to filter by. Default is "features".

### Value

A list of `data.frame`'s or a `SummarizedExperiment`. If a `data.frame` was originally input into the `CytoK` function, a list with two elements, `DEdata`, `nonDEfeatures`, will be returned. If a `SummarizedExperiment` was originally input, output will be a `SummarizedExperiment` with the filtered assay with one metadata object `nonDEfeatures` and four row meta-data `EffectSize`, `EffectSizeSD`, `pvalue` and `padj`.

### 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)
    CytoKDEData(data_CytoK, by = "features")

[Package cytoKernel version 1.0.0 Index]