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Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI)

Source: R/bootTEI.R
bootTEI.Rd

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

Value

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

Details

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

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

Author

Kristian K Ullrich

Examples


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

# computing partial TEI contribution per gene
bM <- bootTEI(PhyloExpressionSetExample)