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Compute Partial Transcriptome Evolutionary Index (TEI) Strata Values

Source: R/pStrataTEI.R
pStrataTEI.Rd

This 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 \(ps\).

Usage

pStrataTEI(
  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

Value

a numeric matrix storing the summed partial TEI values for each strata.

Details

The partial TEI values combined per strata give an overall impression of the contribution of each strata 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

Author

Kristian K Ullrich

Examples


# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample, package = "myTAI")

# computing partial TEI contribution per gene
pS <- pStrataTEI(PhyloExpressionSetExample)