myTAI (version 0.9.3)

TPI: Compute the Transcriptome Polymorphism Index (TPI)

Description

This function computes the Transcriptome Polymorphism Index (TPI) introduced by Gossmann et al., 2015.

Usage

TPI(PolymorphismExpressionSet)

Arguments

PolymorphismExpressionSet

a standard PolymorphismExpressionSet object.

Value

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

Details

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.

References

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.

See Also

TAI, TDI, PlotSignature, PlotPattern, FlatLineTest, ReductiveHourglassTest

Examples

# NOT RUN {
# reading a standard PolymorphismExpressionSet
data(PolymorphismExpressionSetExample)

# computing the TPI profile of a given PolymorphismExpressionSet object
TPIs <- TPI(PolymorphismExpressionSet)
# }
# NOT RUN {

# }