CytoK-class: the CytoK class

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

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)

Ghoshlab/cytoKernel documentation built on Dec. 17, 2021, 9:32 p.m.