local_test_factory {Category} | R Documentation |
These functions return functions appropriate for use as the
tfun
argument to topdown_tree_visitor
or bottomup_tree_visitor
.
In particular, it is these functions that are associated with the
"local" and "global" options for the type
argument to
cb_test
.
local_test_factory(selids, tableTest = chisq.test) hg_test_factory(selids, PCUT = 0.05, COND = FALSE, OVER = TRUE)
selids |
A vector of gene IDs. The IDs should match those used
to annotatate the ChrBandTree given by chrtree . In most
cases, these will be Entrez Gene IDs. |
tableTest |
A contingency table testing function. The behavior
of this function must be reasonably close to that of chisq.test . |
PCUT |
A p-value cutoff that will be used to determine if a given
test is significant or not when using hg_test_factory
with COND=TRUE . |
COND |
A logical value indicating whether a conditional test should be performed. |
OVER |
If TRUE , test for over representation, if FALSE ,
test for under representation. |
The returned functions have signature f(start, g, prev_ans)
where start
is a vector of start nodes, g
is a
chromosome band tree graph, and prev_ans
can contain the
previous result returned by a call to this function.
A function that can be used as the tfun
argument to the tree
visitor functions.
Seth Falcon