RE {myTAI} | R Documentation |
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
Examples
# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
# relative expression profile of PS1 genes
RE(PhyloExpressionSetExample[ which(PhyloExpressionSetExample[ , 1] == 1), 3:9 ])