examplePosets: Example posets

In OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis

Description

Some example posets. For simplicity, all the posets are in a single list. You can access each poset by accessing each element of the list. The first digit or pair of digits denotes the number of nodes.

Poset 1101 is the same as the one in Gerstung et al., 2009 (figure 2A, poset 2). Poset 701 is the same as the one in Gerstung et al., 2011 (figure 2B, left, the pancreatic cancer poset). Those posets were entered manually at the command line: see poset.

Usage

data("examplePosets")

Format

The format is: List of 13 $ p1101: num [1:10, 1:2] 1 1 3 3 3 7 7 8 9 10 ... $ p1102: num [1:9, 1:2] 1 1 3 3 3 7 7 9 10 2 ... $ p1103: num [1:9, 1:2] 1 1 3 3 3 7 7 8 10 2 ... $ p1104: num [1:9, 1:2] 1 1 3 3 7 7 9 2 10 2 ... $ p901 : num [1:8, 1:2] 1 2 4 5 7 8 5 1 2 3 ... $ p902 : num [1:6, 1:2] 1 2 4 5 7 5 2 3 5 6 ... $ p903 : num [1:6, 1:2] 1 2 5 7 8 1 2 3 6 8 ... $ p904 : num [1:6, 1:2] 1 4 5 5 1 7 2 5 8 6 ... $ p701 : num [1:9, 1:2] 1 1 1 1 2 3 4 4 5 2 ... $ p702 : num [1:6, 1:2] 1 1 1 1 2 4 2 3 4 5 ... $ p703 : num [1:6, 1:2] 1 1 1 1 3 5 2 3 4 5 ... $ p704 : num [1:6, 1:2] 1 1 1 1 4 5 2 3 4 5 ... $ p705 : num [1:6, 1:2] 1 2 1 1 1 2 2 5 4 6 ...

Source

Gerstung et al., 2009. Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics, 21: 2809–2815.

Gerstung et al., 2011. The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis. PLoS ONE, 6.

See Also

poset

Examples

data(examplePosets)

## Plot all of them
par(mfrow = c(3, 5))

invisible(sapply(names(examplePosets),
                 function(x) {plotPoset(examplePosets[[x]],
                     main = x,
                     box = TRUE)}))

OncoSimulR documentation built on Nov. 8, 2020, 8:31 p.m.