cb_contingency {Category} | R Documentation |
For each chromosome band identifier in 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)
selids |
A vector of the selected gene identifiers (usual Entrez IDs). |
chrVect |
A character vector of chromosome band identifiers |
chrGraph |
A 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. |
testFun |
The function to use for testing the 2 x k contingency
tables. The default is chisq.test . It will be called with a
single argument, a 2 x k matrix representing the contingency table. |
min.expected |
A numeric value specifying the minimum expected
count for columns to be included in the contingency table. The
expected count is (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. |
min.k |
An integer giving the minimum number of chromosome bands that must be present in a contingency table in order to proceed with testing. |
b |
A list as returned by cb_contingency |
p.value |
A p-value cutoff to use in selecting significant contingency tables. |
n |
A length one character vector specifying a chromosome band
annotation. Bands not found in chrGraph will return
character(0) when passed to cb_children . |
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
.
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:
table |
A 2 x k contingency table |
result |
The output of 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
.
Seth Falcon