maxGap-method {biovizBase} | R Documentation |
Compute an estimated max gap information, which could
be used as max.gap argument in shringkageFun
.
## S4 method for signature 'GenomicRanges' maxGap(obj, ratio = 0.0025)
obj |
GenomicRanges object |
ratio |
Multiple by the range of the provided gaps as the max gap. |
This function tries to estimate an appropriate max gap to be used for creating a shrinkage function.
A numeric value
Tengfei Yin
require(GenomicRanges) gr1 <- GRanges("chr1", IRanges(start = c(100, 300, 600), end = c(200, 400, 800))) gr2 <- GRanges("chr1", IRanges(start = c(100, 350, 550), end = c(220, 500, 900))) gaps.gr <- intersect(gaps(gr1, start = min(start(gr1))), gaps(gr2, start = min(start(gr2)))) shrink.fun <- shrinkageFun(gaps.gr, max.gap = maxGap(gaps.gr)) shrink.fun(gr1) shrink.fun(gr2)