Top quantile expression genes

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

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" )
#> Plot signature: ' TAI ' and test statistic: ' FlatLineTest ' running  1000  permutations.
#> 
#> [ Number of Eigen threads that are employed on your machine: 12 ]
#> 
#> [ Computing age assignment permutations for test statistic ... ]
#> 
[=========================================] 100%   
#> [ Computing variances of permuted transcriptome signatures ... ]
#> 
#> 
#> Total runtime of your permutation test: 0.132  seconds.
#> 
#> -> We recommended using at least 20000 permutations to achieve a sufficient permutation test.
#> 
#> Significance status of signature:  significant.
#> 
#> -> Now run 'FlatLineTest(..., permutations  = 1000, plotHistogram = TRUE)' to analyse the permutation test performance.