concubfilter-class: Class '"concubfilter"'
In geecc: Gene Set Enrichment Analysis Extended to Contingency Cubes

Description Details Objects from the Class Slots Methods and slot accessors Examples

An object of type concubfilter

The large number of different filter options (and corresponding getter and setter accessors) makes it necessary to maintain them in a special class. This differs from other packages like GOstats, where arguments for controlling the program and the results are stored in the same object.

Objects can be created by calls of the form new("concubfilter", ...).

For a more detailed description of some slots see below.

nfact:: a numeric giving the number of factors
names:: a character vector giving the name of each factor
p.value:: a numeric giving the P-value to be considered. Defaults to 0.1.
test.direction:: a character giving the direction of association. Defaults to “two.sided”.
minimum.l2or:: a numeric giving the minimum absolute log2 odds ratio to be considered. Defaults to 0.
skip.min.group:: a numeric giving the minimum number of tag a group is allowed to have. Defaults to 2.
skip.min.obs:: a numeric giving the minimum number at the position of interest allowed. Defaults to 2.
skip.zeroobs:: a logical. Defaults to TRUE.
drop.insignif.layer:: A vector of logicals. By default, all positions are set to FALSE.
drop.wrongdir.layer:: A vector of logicals. By default, all positions are set to FALSE.
drop.lowl2or.layer:: A vector of logicals. By default, all positions are set to FALSE.

Several methods are implemented for class concubfilter. They can be roughly grouped into informative, basic, skip-test, and data-reduction methods.

Individual options can be accessed by the corresponding getter and setter methods, for instance

skip.zeroobs: signature(x = "concubfilter"): get current setting to skip test in case of zero cell
skip.zeroobs<-: signature(x = "concubfilter"): set a new value to skip test in case of zero cell

Informative methods

Currently only a single method is implemented.

show: signature(object = "concubfilter"): a short summary about current filter settings

Basic filters/threshoulds

p.value: The maximum P-value that should be taken into account
minimum.l2or: The minumum absolute of log2 odds ratio that should be taken into account
test.direction: The direction of the association. Can be “two.sided”, “greater” (test for over-representation), or “less” (test for under-representation)

Skip test

The following filters cause a skip of a test, i.e. the test is never run if at least one of the conditions is fullfilled.

skip.zeroobs: skip the test, if the position of interest (x_{00} or x_{000}) is zero, i.e. no tag from the population matches the conditions defined at the marginals.
skip.mingroup: skip the test, if the groups considered at the position of interest are too small at all.
skip.minobs: skip the test, if the position of interest contains less than ‘this value’ entries.

Data reduction

The following filters reduce the amout of outcome of the tests. They are applied to both, the (2 or 3 dimensional) table containing the odds ratios and the table containing the corresponding P-values.

drop.insignif.layer: drop all layers in the tables where all P-values are greater than the value defined in ‘p.value’.
drop.wrongdir.layer: drop all layers in the tables where all odds ratios are showing into the opposite direction as defined in ‘test.direction’.
drop.lowl2or.layer: drop all layers in the tables where all absolutes of the log2 odds ratios are smaller than ‘min.l2or’.