RE: Transform to Relative Expression Levels
In YTLogos/myTAI: Evolutionary Transcriptomics

Description Usage Arguments Value Author(s) References See Also Examples

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.

1	RE(ExpressionMatrix)

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.

Hajk-Georg Drost

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.

REMatrix, PlotRE

# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)

# relative expression profile of PS1 genes
RE(PhyloExpressionSetExample[ which(PhyloExpressionSetExample[ , 1] == 1), 3:9 ])