myTAI (version 0.9.3)

REMatrix: Compute a Relative Expression Matrix

Description

This function computes the relative expression profiles of all given phylostrata or divergence-strata within a given PhyloExpressionSet or DivergenceExpressionSet.

Usage

REMatrix(ExpressionSet)

Arguments

ExpressionSet

a standard PhyloExpressionSet or DivergenceExpressionSet object.

Details

For each phylostratum or divergence-stratum the corresponding relative expression profile is being computed as follows:

$$f_js = ( e_js - e_j min ) / ( e_j max - e_j min )$$

where \(e_j min\) and \(e_j max\) denote the minimum/maximum mean expression level of phylostratum j over the developmental stages s. This linear transformation corresponds to a shift by \(e_j min\) and a subsequent shrinkage by \(e_j max - e_j min\). As a result, the relative expression level \(f_js\) of developmental stage s with minimum \(e_js\) is 0, the relative expression level \(f_js\) of the developmental stage s with maximum \(e_js\) is 1, and the relative expression levels \(f_js\) of all other stages s range between 0 and 1, accordingly.

References

Domazet-Loso T and Tautz D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (468): 815-818.

Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101.

See Also

RE, PlotRE, PlotBarRE

Examples

# NOT RUN {
# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

# example PhyloExpressionSet
REMatrix(PhyloExpressionSetExample)

# example DivergenceExpressionSet
REMatrix(DivergenceExpressionSetExample)


# }