CytoKFeaturesOrdered: Generic function that returns the ordered CytoK features

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

Generic function that returns the ordered CytoK features

Description

Given a CytoK object, this function returns the CytoK features ordered by adjusted p values

Accessors for the 'CytoKFeaturesOrdered' slot of a CytoK object.

Usage

CytoKFeaturesOrdered(object)

## S4 method for signature 'CytoK'
CytoKFeaturesOrdered(object)

Arguments

object

an object of class CytoK.

Value

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.

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)
CytoKFeaturesOrdered(data_CytoK)

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