penetrance: Penetrance computation from a series of segments
In cghRA: Array CGH Data Analysis and Visualization

This function computes the penetrance of various states from a parallelized series of segments.

In each point of the genome, the penetrance is the proportion of the series arrays that show a specific alteration state.

1 2	penetrance(segParallel, states = list(deletion=c(-Inf, -0.5), gain=c(0.5, Inf)), na = c("fill", "keep", "false"), mergeOnValue = FALSE, bool = FALSE, quiet = FALSE)

`segParallel`	A `data.frame`, as returned by `parallelize`.
`states`	A named `list` of numerics defining the boundaries of each state. Each state may be defined by a single value (the only value in `segParallel` to link to the state) or by two boundaries (the lower boundary is part of the state, the upper one is not). `Inf` and `-Inf` can be used as boundaries.
`na`	Single character value defining how to deal with `NA` segments : "fill" fills them when possible (chromosome ends and gaps for which the state is the same on each side), "keep" keeps all of them `NA` and "false" always considers them as "not in the state". When `NA` remains ("fill" or "keep"), the penetrance frequency is locally computed on non-`NA` samples.
`mergeOnValue`	Single logical value, whether to merge consecutive regions with same penetrance value but distinct alterated sample list.
`bool`	Single logical value, if `TRUE` the penetrance is not returned but logical matrixes of regions 'in state' are returned instead. This is a quite uncommon behavior, allowed essentially for code recycling by other packages, use `FALSE`.
`quiet`	Single logical value, whether to throw diagnosis messages or not.

If bool is FALSE, a list containing a distinct data.frame for each state, with the following columns :

`chrom`	Character, the chromosomal location of the region described.
`start`	Integer, the lower coordinate of the region described.
`end`	Integer, the upper coordinate of the region described.
`value`	Numeric, the penetrance in the region described for the state described.