Usage
cb_test(selids, chrtree, level, dir = c("up", "down"), type = c("local", "global"), next.pval = 0.05, cond.pval = 0.05, conditional = FALSE)
Arguments
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.
chrtree
A ChrBandTree object representing the chromosome
bands and the mapping to gene identifiers. The genes in the
ChrBandTree are limited to the universe of gene IDs specified
at object creation time.
level
An integer giving the level of the chromosome band tree
at which testing should begin. The level is conceptualized as the set
of nodes with a given path length to the root (organism) node of the
chromosome band tree. So level 1 is the chromosome and level 2 is the
chromosome arms. You can get a better sense by calling
exampleLevels(chrtree)
dir
A string giving the direction in which the chromosome band
tree will be traversed when carrying out the tests. A bottom up
traversal, from leaves to root, is specified by "up". A top
down, from root to leaves, traversal is specified by "down".
type
A string giving the type of test to perform. The current
choices are "local" and "global". A local test
carries out a chisq.test on each 2 x K contingency table induced by
each set of siblings at a given level in the tree. A global test
uses the Hypergeometric distribution to compute a p-value for the 2
x 2 tables induced by each band treated independently.
next.pval
The p-value cutoff used to determine whether the parents
or children of a node should be tested. After testing a given level
of the tree, the decision of whether or not to continue testing the
children (or parents) of the already tested nodes is made by
comparing the p-value result for a given node with this cutoff;
relatives of nodes with values strictly greater than the cutoff are
skipped.
cond.pval
The p-value cutoff used to determine whether a node
is significant during a conditional test. See conditional.
conditional
A logical value. Can only be used when
dir="up" and type="global". In this case, a
TRUE value causes a conditional Hypergeometric calculation to
be performed. The genes annotated at significant children of a
given band are removed before testing.