R/pStrataTEI.R
pStrataTEI.RdThis function computes the partial transcriptome evolutionary index (TEI) values combined for each strata.
In detail, each gene gets a TEI contribution profile.
$$TEI_{is} = f_{is} * ps_i$$
where \(TEI_{is}\) is the partial TEI value of gene i, \(f_{is} = e_{is} / \sum e_{is}\) and \(ps_i\) is the phylostratum of gene i.
\(TEI_{is}\) values are combined per \(ps\).
pStrataTEI(
ExpressionSet,
Phylostratum = NULL,
split = 1e+05,
showprogress = TRUE,
threads = 1
)expression object with rownames as GeneID (dgCMatrix) or standard PhyloExpressionSet object.
a named vector representing phylostratum per GeneID with names as GeneID (not used if Expression is PhyloExpressionSet).
specify number of columns to split
boolean if progressbar should be shown
specify number of threads
a numeric matrix storing the summed partial TEI values for each strata.
The partial TEI values combined per strata give an overall
impression of the contribution of each
strata to the global TEI pattern.
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
# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample, package = "myTAI")
# computing partial TEI contribution per gene
pS <- pStrataTEI(PhyloExpressionSetExample)