local_test_factory: Local and Global Test Function Factories
In Category: Category Analysis

Description Usage Arguments Details Value Author(s) See Also

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.

1 2	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

cb_test

Category documentation built on Nov. 8, 2020, 10:58 p.m.