CytoKDEData: Differentially expressed data by cytoKernel

In Ghoshlab/cytoKernel: Differential expression using kernel-based score test

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")

Ghoshlab/cytoKernel documentation built on Nov. 24, 2024, 9:17 a.m.