This function computes the partial transcriptome evolutionary index (TEI) values for each single gene.
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.
Usage
pMatrixTEI(
ExpressionSet,
Phylostratum = NULL,
split = 1e+05,
showprogress = TRUE,
threads = 1
)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 partial TEI matrix can be used to perform different cluster
analyses and also gives an overall impression of the contribution of each
gene to the global TEI pattern.
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 partial TEI contribution per gene
pMT <- pMatrixTEI(PhyloExpressionSetExample)