This function computes the relative expression profiles of any given gene expression set. The relative expression profile is being computed as follows:
$$f_s = ( e_s - e_min ) / ( e_max - e_min )$$
where \(e_min\) and \(e_max\) denote the minimum/maximum mean expression level over the developmental stages s. This linear transformation corresponds to a shift by \(e_min\) and a subsequent shrinkage by \(e_max - e_min\). As a result, the relative expression level \(f_s\) of developmental stage s with minimum \(e_s\) is 0, the relative expression level \(f_s\) of the developmental stage s with maximum \(e_s\) is 1, and the relative expression levels \(f_s\) of all other stages s range between 0 and 1, accordingly.
RE(ExpressionMatrix)a numeric matrix representing a gene expression matrix for which the relative expression profile shall be computed.
a vector containing the relative expression profile of the correspnding data matrix.
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.
# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
# relative expression profile of PS1 genes
RE(PhyloExpressionSetExample[ which(PhyloExpressionSetExample[ , 1] == 1), 3:9 ])
#> Zygote Quadrant Globular Heart Torpedo Bent Mature
#> 0.4816246 0.3145330 0.4638918 0.0000000 0.1706749 0.5688023 1.0000000