distribution.oncotree: Find the event distribution defined by an oncogenetic tree In Oncotree: Estimating oncogenetic trees

Description

`distribution.oncotree` calculates the joint distribution of the events defined by the tree, while `marginal.distr` calculates the marginal probability of occurrence of each event.

Usage

 ```1 2 3 4``` ``` distribution.oncotree(otree, with.probs = TRUE, with.errors=FALSE, edge.weights=if (with.errors) "estimated" else "observed") marginal.distr(otree, with.errors = TRUE, edge.weights=if (with.errors) "estimated" else "observed") ```

Arguments

 `otree` An object of class `oncotree`. `with.probs` A logical value specifying if only the set of possible outcomes should be returned (if TRUE), or the associated probabilities of occurrence as well. `with.errors` A logical value specifying whether false positive and negative error rates should be incorporated into the distribution. `edge.weights` A choice of whether the observed or estimated edge transition probabilities should be used in the calculation of probabilities. See `oncotree.fit` for explanation of the difference. By default, estimated edge transition probabilies if `with.errors=TRUE` and the observed ones if `with.errors=FALSE`.

Value

For `distribution.oncotree`: a data frame each row of which gives a possible outcome.

For `marginal.distr`: a named numeric vector - the names are the event names (+ ‘Root’) and the values are the corresponding marginal probability of occurrence.

Author(s)

Aniko Szabo

`oncotree.fit`

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20``` ``` data(ov.cgh) ov.tree <- oncotree.fit(ov.cgh) #joint distribution jj <- distribution.oncotree(ov.tree, edge.weights="obs") head(jj) jj.eps <- distribution.oncotree(ov.tree, with.errors=TRUE) head(jj.eps) #marginal distribution marginal.distr(ov.tree, with.error=FALSE) #marginal distribution calculated from the joint apply(jj[1:ov.tree\$nmut], 2, function(x){sum(x*jj\$Prob)}) ##Same with errors incorporated #marginal distribution marginal.distr(ov.tree, with.error=TRUE) #marginal distribution calculated from the joint apply(jj.eps[1:ov.tree\$nmut], 2, function(x){sum(x*jj.eps\$Prob)}) ```

Oncotree documentation built on May 31, 2017, 3:04 a.m.