local_test_factory

hg_test_factory

A vector of gene IDs.  The IDs should match those used
    to annotatate the <code>ChrBandTree</code> given by <code>chrtree</code>.  In most
    cases, these will be Entrez Gene IDs.

selids

A contingency table testing function.  The behavior
    of this function must be reasonably close to that of <code>chisq.test</code>.

tableTest

A p-value cutoff that will be used to determine if a given
    test is significant or not when using <code>hg_test_factory</code>
    with <code>COND=TRUE</code>.

PCUT

A logical value indicating whether a conditional test
  should be performed.

COND

If <code>TRUE</code>, test for over representation, if <code>FALSE</code>,
    test for under representation.

OVER


  These functions return functions appropriate for use as the
  <code>tfun</code> argument to <code>topdown_tree_visitor</code> or <code>bottomup_tree_visitor</code>.
  In particular, it is these functions that are associated with the
  "local" and "global" options for the <code>type</code> argument to
  <code>cb_test</code>.


internal

A collection of tools for performing category analysis.

Bioconductor Package Maintainer

Category Analysis

local_test_factory function

These functions return functions appropriate for use as the
  <code>tfun</code> argument to <code>topdown_tree_visitor</code> or <code>bottomup_tree_visitor</code>.
  In particular, it is these functions that are associated with the
  "local" and "global" options for the <code>type</code> argument to
  <code>cb_test</code>.

local_test_factory: Local and Global Test Function Factories

Description

Usage

Arguments

Value

Details

See Also