chrVect
,
cb_contingency
builds and performs a test on a 2 x k
contingency table for the genes from selids
found in the child
bands of the given chrVect
element. cb_sigBands
extracts the chromosome band identifiers that were
in a contingency table that tested significant given the specified
p-value cutoff.
cb_children
returns the child bands of a given band in the
chromosome band graph. The argument must have length equal to one.
cb_contingency(selids, chrVect, chrGraph, testFun = chisq.test, min.expected = 5L, min.k = 1L)
cb_sigBands(b, p.value = 0.01)
cb_children(n, chrGraph)
graph
object as returned by
makeChrBandGraph
. The nodes should be chromosome band IDs
and the edges should represent the tree structure of the bands.
Furthermore, the graph is expected to have a "geneIds"
node
attribute providing a vector of gene IDs annotated at each band.chisq.test
. It will be called with a
single argument, a 2 x k matrix representing the contingency table.(rowSum * colSum) / n
. Chromosome bands
with a select cell count less than min.expected
are dropped
from the table before testing occurs. If NULL
, then no bands
will be dropped.cb_contingency
chrGraph
will return
character(0)
when passed to cb_children
.cb_contingency
returns a list with an element for each test
performed. This will most often be shorter than
length(chrVect)
due to skipped tests based on min.found
and min.k
. Each element of the returned list is itself a list
with components:
testFun
applied to the table
.cb_sigBands
returns a character vector of chromosome band
identifiers that are in one of the contingency tables that had a
p-value less than the cutoff specified by p.value
.
cb_sigBands
assumes that the p-value associated with a result
of testFun
can by accessed as testFun(t)$p.value
. We
should improve this to be a method call which can then be specialized
based on the class of the object returned by testFun
.