TAI: Compute the Transcriptome Age Index (TAI)

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/TAI.R

Description

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

Usage

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TAI(PhyloExpressionSet)

Arguments

PhyloExpressionSet

a standard PhyloExpressionSet object.

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 = ∑ (e_is * ps_i) / ∑ 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.

Value

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

Author(s)

Hajk-Georg Drost

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) Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis. Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012.

See Also

TDI, PlotPattern, FlatLineTest, ReductiveHourglassTest

Examples

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# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample)

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

myTAI documentation built on July 4, 2017, 9:09 a.m.