Description Usage Arguments Value Examples
This function generate an inversed variance matrix from expression profiles of one-to-one orthologous genes across species
This function esitmates ancestral expression profile and related statistical uncertainty
1 2 3 |
objects |
a vector of objects of class |
phy |
an rooted expression character tree |
taxa |
oen single character or a vector of characters sepcifying taxa to generate
an inversed variance matrix.
If one single character "all" is given,
all the taxa included in the |
subtaxa |
one single character specifying sub taxa to be included in generating an inversed variance matrix |
x |
a vector of known expression profile, preferably log-transformed expression levels (e.g. log RPKM) |
mat |
a matrix generated from "varMatInv" function |
select |
indicate if descendents of the node or all tips should be used |
CI |
a logical specifying whether to return the 95 of the estimated ancestral expression levels |
phy |
a phylogenetic tree in the form of object "phylo" |
returns an inversed variance matrix
returns a list containing estimated ancestral expression profile as well as other requested parameters
1 2 3 4 5 6 7 8 9 10 | data('tetraexp')
dismat <- expdist(tetraexp.objects, taxa = "all", subtaxa = "Brain", method = "sou")
exp_tree <- NJ(dismat)
exp_tree <- root(exp_tree, outgroup = "Chicken_Brain", resolve.root = T)
exp_tree <- no0br(exp_tree)
var_mat <- varMatInv(objects = tetraexp.objects,phy = exp_tree,taxa = "all", subtaxa = "Brain")
exp_table <- exptabTE(tetraexp.objects, taxa = "all", subtaxa = "Brain")
exp_one <- aee(exp_table[1,], exp_tree, var_mat)
exp_tree$node.label <- exp_one$est
plot(exp_tree)
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