This function computes the Transcriptome Polymorphism Index (TPI) introduced by Gossmann et al., 2015.
TPI(PolymorphismExpressionSet)a standard PolymorphismExpressionSet object.
a numeric vector containing the TPI values for all given developmental stages.
The TPI measure represents the weighted arithmetic mean (expression levels as weights) for the synonymous vs non-synonymous polymorphism ratios.
$$TPI_s = \sum (e_is * P_N/N / ((P_S + 1) / S)) / \sum e_is$$
where TPI_s denotes the TPI value in developmental stage s, e_is denotes the gene expression level of gene i in stage s, n denotes the number of genes, PN and PS denote the numbers of non-synonymous and synonymous polymorphisms, and N and S are the numbers of nonsynonymous and synonymous sites, respectively.
Internally the function is written in C++ to speed up TPI computations.
Gossmann et al. (2015). Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes. Mol Biol Evol. 33 (7): 1669-1678.
if (FALSE) {
# reading a standard PolymorphismExpressionSet
data(PolymorphismExpressionSetExample)
# computing the TPI profile of a given PolymorphismExpressionSet object
TPIs <- TPI(PolymorphismExpressionSet)
}