pMatrixTEI: Compute Partial Transcriptome Evolutionary Index (TEI) Values

In HajkD/myTAI: Evolutionary Transcriptomics

Compute Partial Transcriptome Evolutionary Index (TEI) Values

Description

This function computes the partial transcriptome evolutionary index (TEI) values for each single gene.

In detail, each gene gets a TEI contribution profile.

TEI_{is} = f_{is} * ps_i

where TEI_{is} is the partial TEI value of gene i, f_{is} = e_{is} / \sum e_{is} and ps_i is the phylostratum of gene i.

Usage

pMatrixTEI(
  ExpressionSet,
  Phylostratum = NULL,
  split = 1e+05,
  showprogress = TRUE,
  threads = 1
)

Arguments

ExpressionSet	expression object with rownames as GeneID (dgCMatrix) or standard PhyloExpressionSet object.
Phylostratum	a named vector representing phylostratum per GeneID with names as GeneID (not used if Expression is PhyloExpressionSet).
split	specify number of columns to split
showprogress	boolean if progressbar should be shown
threads	specify number of threads

Details

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

Value

a numeric sparse matrix storing the partial TEI values for each gene.

Author(s)

Kristian K Ullrich

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

Examples

# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample, package = "myTAI")

# computing partial TEI contribution per gene
pMT <- pMatrixTEI(PhyloExpressionSetExample)

HajkD/myTAI documentation built on April 6, 2024, 7:47 p.m.