| TAI {myTAI} | R Documentation |
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. |
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.
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) Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012
See Also
TDI, PlotPattern, FlatLineTest, ReductiveHourglassTest
Examples
# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample)
# computing the TAI profile of a given PhyloExpressionSet object
TAIs <- TAI(PhyloExpressionSetExample)