TEI | R Documentation |
This function computes the phylogenetically based transcriptome evolutionary index (TEI) similar to Domazet-Loso & Tautz, 2010.
TEI(
ExpressionSet,
Phylostratum = NULL,
split = 1e+05,
showprogress = TRUE,
threads = 1
)
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 |
The TEI measure represents the weighted arithmetic mean (expression levels as weights for the phylostratum value) over all evolutionary age categories denoted as phylostra.
TEI_s = \sum (e_is * ps_i) / \sum e_is
where TEI_s denotes the TEI value in developmental stage s,
e_is denotes the gene expression level of gene i in stage s,
and ps_i denotes the corresponding phylostratum of gene i,
i = 1,...,N
and N = total number of genes.
a numeric vector containing the TEI values for all given cells or developmental stages.
Kristian K Ullrich
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
# reading a standard PhyloExpressionSet
data(PhyloExpressionSetExample, package = "myTAI")
# computing the TEI profile of a given PhyloExpressionSet object
TEI <- TEI(PhyloExpressionSetExample)
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