bootTEI: Compute a Permutation Matrix of Transcriptome Evolutionary...

In HajkD/myTAI: Evolutionary Transcriptomics

Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI)

Description

This function computes the transcriptome evolutionary index (TEI) using permuted strata values.

Usage

bootTEI(
  ExpressionSet,
  Phylostratum = NULL,
  permutations = 100,
  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).
permutations	a numeric value specifying the number of permutations to be performed.
split	specify number of columns to split
showprogress	boolean if progressbar should be shown
threads	specify number of threads

Details

The strata values are sampled and the global TEI is calculated N times.

Value

a numeric matrix storing the TEI values based on permuted strata.

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
bM <- bootTEI(PhyloExpressionSetExample)

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