REMatrix {myTAI} | R Documentation |
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.
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)
data(DivergenceExpressionSetExample)
# example PhyloExpressionSet
REMatrix(PhyloExpressionSetExample)
# example DivergenceExpressionSet
REMatrix(DivergenceExpressionSetExample)