rcpp_boottei_parallel | R Documentation |
computes the phylogenetically based transcriptome evolutionary index (TEI) shuffling the strata for permutation statistic
rcpp_boottei_parallel(expression, ps, permutations, ncores = 1L)
expression |
ExpressionSet as sparseMatrix |
ps |
named Phylostratum |
permutations |
number of permutations |
ncores |
number of cores |
sparseMatrix
Kristian K Ullrich
## load example PhyloExpressionSetExample
data("PhyloExpressionSetExample", package="myTAI")
## convert into sparseMatrix - rownames GeneID
spmat <- as(data.matrix(PhyloExpressionSetExample[,-c(1,2)]),
"sparseMatrix")
rownames(spmat) <- PhyloExpressionSetExample$GeneID
## create named Phylostratum vector
ps <- setNames(PhyloExpressionSetExample$Phylostratum,
PhyloExpressionSetExample$GeneID)
## get permutations
rcpp_boottei_parallel(spmat, ps, 100, 1)
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