This function computes the phylogenetically based transcriptome evolutionary index (TEI) similar to Domazet-Loso & Tautz, 2010.
Arguments
- ExpressionSet
expression object with rownames as GeneID (dgCMatrix) or standard PhyloExpressionSet object.
- Phylostratum
a named vector representing phylostratum per GeneID with names as GeneID (not used if Expression is PhyloExpressionSet).
- split
specify number of columns to split
- showprogress
boolean if progressbar should be shown
- threads
specify number of threads
Details
The TEI measure represents the weighted arithmetic mean (expression levels as weights for the phylostratum value) over all evolutionary age categories denoted as phylostra.
$$TEI_s = \sum (e_is * ps_i) / \sum e_is$$
where TEI_s denotes the TEI value in developmental stage s, e_is denotes the gene expression level of gene i in stage s, and ps_i denotes the corresponding phylostratum of gene i, \(i = 1,...,N\) and N = total number of genes.
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.
Drost HG et al. (2015) Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012
Examples
# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample, package = "myTAI")
# computing the TEI profile of a given PhyloExpressionSet object
TEI <- TEI(PhyloExpressionSetExample)