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pneuvial / c3co

Inferring cancer cell clonality from copy-number data
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Avoid relying on 'minMaxPos' #17

Closed pneuvial closed 7 years ago

pneuvial commented 7 years ago

Currently 'createZdf' requires an argument 'minMaxPos', a matrix containing min and max position for each chromosome. This should really be taken care of by the package, not by the user.

If we add to the slot 'bkp' of a fitC3co object a "first breakpoint" at the first position and a "last breakpoint" at the last position, then the object will be selfcontained.

pneuvial commented 7 years ago

Fixed [develop 9caaf42]

pneuvial commented 7 years ago

Side effect: we're now plotting the horizontal lines twice in Zplot, cf

    gg <- gg + geom_step(direction="hv", lwd=1)
    gg <- gg + geom_segment(aes_(xend=~end, yend=~CopyNumber), lwd=1)