segmentSeqData: Copy number segmentation

Description Usage Arguments Value Author(s) Examples

View source: R/segmentSeqData.r

Description

Wrapped for function copynumber::pcf to do segmentation.

Usage

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segmentSeqData(rangedata, gamma = 500, kmin = 100, maskmap = 0.8, maskadj = FALSE, skipmeanmap=FALSE )

Arguments

rangedata

Object of class IRange produced by function gcCorrect.

gamma

Penalty for each discontinuity. See ?copynumber::pcf

kmin

Minimum number of bins in each segment. See ?copynumber::pcf

maskmap

Ignore bins with mappability less than this

maskadj

Ignore bins adjacent to bins with mappability less than maskmap. NOT USED.

skipmeanmap

Skip call to meanMapInSeg

Value

Data fram returned by copynumber::pcf, to which is added a column named meanmap, that contains the mean mappability calculated in each segment.

Author(s)

Mathieu Lemire

Examples

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## Not run: 
n<- wigsToRangedData( normalWigFile, gcWigFile, mapWigFile )
nc<-gcCorrect(n) 
n.seg <- segmentSeqData( nc, k=50 , maskmap = 0.8 )

## End(Not run)

mathieu-lemire/celluloid_0.11 documentation built on Aug. 6, 2018, 9:15 a.m.