pMatrixTEI | R Documentation |
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.
pMatrixTEI(
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 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.
a numeric sparse matrix storing the partial TEI values for each gene.
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 partial TEI contribution per gene
pMT <- pMatrixTEI(PhyloExpressionSetExample)
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