RE: Transform to Relative Expression Levels

In HajkD/myTAI: Evolutionary Transcriptomics

Transform to Relative Expression Levels

Description

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.

Usage

RE(ExpressionMatrix)

Arguments

ExpressionMatrix

a numeric matrix representing a gene expression matrix for which the relative expression profile shall be computed.

Value

a vector containing the relative expression profile of the correspnding data matrix.

Author(s)

Hajk-Georg Drost

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

REMatrix, PlotRE

Examples

# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)

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

HajkD/myTAI documentation built on April 6, 2024, 7:47 p.m.