myTAI (version 0.9.3)

TAI: Compute the Transcriptome Age Index (TAI)

Description

This function computes the phylogenetically based transcriptome age index (TAI) introduced by Domazet-Loso & Tautz, 2010.

Usage

TAI(PhyloExpressionSet)

Arguments

PhyloExpressionSet

a standard PhyloExpressionSet object.

Value

a numeric vector containing the TAI values for all given developmental stages.

Details

The TAI measure represents the weighted arithmetic mean (expression levels as weights for the phylostratum value) over all evolutionary age categories denoted as phylostra.

$$TAI_s = \sum (e_is * ps_i) / \sum e_is$$

where TAI_s denotes the TAI 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.

Internally the function calls the C++ function cpp_TAI to speed up TAI computations.

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

See Also

TDI, PlotPattern, FlatLineTest, ReductiveHourglassTest

Examples

# NOT RUN {
# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample)

# computing the TAI profile of a given PhyloExpressionSet object
TAIs <- TAI(PhyloExpressionSetExample)



# }