Description Slots Methods Author(s) See Also Examples
Class for performing hierarchical multiple testing corrections.
tree
:Object of class "matrix"
. The edgelist
for the hypotheses tree.
p.vals
:Object of class "data.frame"
. Each
row correpsonds to an individual hypothesis. The first column
stores the p-values before GBH adjustment, while the second
gives the hFDR adjusted p-values. The hypotheses are sorted
in order of significance according to these GBH adjusted
p-values. The group
column gives the group membership
of each hypothesis, and adj.significnace
codes the
significance of each hypothesis, according to the GBH adjusted
p-values.
alpha
:Object of class "numeric"
. The
level at which the FDR is controlled among children
of each parent node.
signature(.Object = "hypothesesTree")
:
...
Check that the hypotheses tree is correctly initialized. It ensures that the number of unadjusted p-values, hypotheses names, and nodes in the hypotheses tree all agree. It also checks that the hypotheses tree is in fact a tree.
signature(x = "hypothesesTree", y = "ANY")
: ...
Plots the tree of hypotheses and their p-values either before or after adjustment. If a particular node hypothesis was not tested, it is colored grey. If it was tested and rejected, it is green; if it was tested and not rejected, it is shaded blue. The deeper the shade, the lower (more significant) the p-value was.
signature(object = "hypothesesTree")
: ...
This prints the unadjusted and adjusted p-values of the hypotheses tree associated with the HFDR procedure.
signature(object = "hypothesesTree")
:
This prints the most significant adjusted p-values, along with
estimates of the FDR across the tree and at tips.
Kris Sankaran
hFDR.adjust
EstimatedHFDRControl
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | library('igraph')
library('ape')
alternative.indices <- sample(1:49, 30)
unadj.p.values <- vector("numeric", length = 49)
unadj.p.values[alternative.indices] <- runif(30, 0, 0.01)
unadj.p.values[-alternative.indices] <- runif(19, 0, 1)
unadj.p.values[c(1:5)] <- runif(5, 0, 0.01)
names(unadj.p.values) <- paste("Hyp ", c(1:49))
tree <- as.igraph(rtree(25))
V(tree)$name <- names(unadj.p.values)
tree.el <- get.edgelist(tree)
hyp.tree <- hFDR.adjust(unadj.p.values, tree.el, 0.05)
plot(hyp.tree)
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