compareEquivalences {bayesCGH} | R Documentation |
This function compares a set of equivalence relations which define
hypotheses of similarity within and differences between equivalence
classes. The function is intended for use on array CGH data in the form
of a ClassifySegList
object.
seg |
Object of class ClassifySegList . |
group.arrays |
A list object of which each item should be a numeric vector giving the indices of the arrays in 'seg' belonging to a particular clinical set. |
group.names |
Names of the clinical sets defined by 'sel.groups'. |
probe.classes |
A list object of which each item is a character vector that describes the different groups of classifications of the aCGH data. Unlikely to change from default. |
classes |
A list object, of which each item is another list object that defines an equivalence relation on the set of sets defined by 'sel.groups' (see Details). |
class.names |
Names for each equivalence relation defined in 'classes' |
class.priors |
Priors for each equivalence relation defined in 'classes' (see Details). |
X.distinct |
Should the X chromosome be omitted from estimation of the prior? |
Y.distinct |
Should the Y chromosome be omitted from estimation of the prior? |
same.priors |
Do all equivalence relations defined in 'classes' have the same prior Dirichlet distribution on the different classifications defined in 'probe.classes'? |
This function takes a number of subsets of the 'seg' ClassifySegList structure and simultaneously tests a number of hypotheses defined in terms of equivalence classes upon them.
The subsets of 'seg' to be used are defined by 'sel.groups'. This is a list object in which the nth item is a numerical vector giving the arrays belonging to the nth subset. Names of the subsets can be defined in 'group.namess', a string vector.
The 'classes' argument is a list object of which each item is another list object defining an equivalence relation on the sets defined in 'sel.groups'. Names for each equivalence relation can be defined in 'class.names', a string vector. Prior likelihoods of each equivalence relation are defined in 'class.priors'.
List object containing
data |
Description of data submitted to compareEquivalences. |
equivalence.classes |
Description of equivalence classes submitted to compareEquivalences. |
probabilities |
Matrix of probabilities for each probe belonging to each equivalence class. |
Thomas Hardcastle
Hardcastle 2008