TopExpressionGenes: Top quantile expression genes

In HajkD/myTAI: Evolutionary Transcriptomics

Top quantile expression genes

Description

Select genes residing in the top quantile according to the mean of their expression across the stages

Usage

TopExpressionGenes(ExpressionSet, p = 0.99)

Arguments

ExpressionSet	A standard ExpressionSet
p	The quantile probability. Default is p = .99

Value

a character vector containing the gene ids residing in the top expression quantile

Author(s)

Stefan Manolache

Examples

# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample)

# select genes with highest variance (top 2%)  
genes.top_expression <- TopExpressionGenes(PhyloExpressionSetExample, p=.98)

# remove top genes from the PhyloExpressionSet
PhyloExpressionSet.top_removed <- subset(PhyloExpressionSetExample, 
                                         !(GeneID %in% genes.top_expression))

# plot TAI of set with removed quantile
PlotSignature(ExpressionSet = PhyloExpressionSet.top_removed,
                measure       = "TAI", 
                TestStatistic = "FlatLineTest",
                xlab          = "Ontogeny", 
                ylab          = "TAI" )

HajkD/myTAI documentation built on June 8, 2025, 10:24 p.m.