pMatrix: Compute Partial TAI or TDI Values

Description Usage Arguments Details Value Author(s) References Examples

Description

This function computes the partial TAI or TDI values for each single gene in a PhyloExpressionSet or DivergenceExpressionSet object.

In detail, each gene gets a TAI contribution profile or TDI contribution profile.

TAI_is = f_is * ps_i

or

TDI_is = f_is * ps_i

where TAI_is or TDI_is is the partial TAI or TDI value of gene i, f_is = e_is / ∑ e_is and ps_i is the phylostratum or divergence-stratum of gene i.

Usage

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pMatrix(ExpressionSet)

Arguments

ExpressionSet

a standard PhyloExpressionSet or DivergenceExpressionSet object.

Details

The partial TAI or TDI matrix can be used to perform different cluster analyses and also gives an overall impression of the contribution of each gene to the global TAI or TDI pattern.

Value

a numeric matrix storing the partial TAI or TDI values for each gene in the corresponding PhyloExpressionSet or DivergenceExpressionSet.

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.

Examples

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# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

# example PhyloExpressionSet
PTM_ps <- pMatrix(PhyloExpressionSetExample)

# example DivergenceExpressionSet
PTM_ds <- pMatrix(DivergenceExpressionSetExample)

# boxplot of the pMatrix
boxplot(pMatrix(PhyloExpressionSetExample),outline = FALSE)

# boxplot of the pMatrix using log2 transformed expression levels
boxplot(pMatrix(tf(PhyloExpressionSetExample,log2)))


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