scaleReadCounts: Scale read counts

Description Usage Arguments Details Author(s) Examples

View source: R/scaleReadCounts.r

Description

Scale gc- and mappability-corrected read counts to absolute copy number.

Usage

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scaleReadCounts(tumourrangedata, epp)

Arguments

tumourrangedata

Object of class IRanges containing tumour data, obtained from a call to gcCorrect

epp

Expected peak positions. Data frame returned by ePeakPos.

Details

An additional column named icopy is added to tumourrangedata (tumourrangedata$icopy). Scaling is done by using the relationship given in epp: each integer copy number configurations in tumour (m1,p1,m2,p2,etc) is associated with the expected gc- and mappability-corrected read count (in x). Values for icopy are in the copy-number scale (as opposed to tumourrangedata$copy which is in a log scale).

Author(s)

Mathieu Lemire

Examples

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## Not run: 
prepCN(12)
ePP<-ePeakPos( S=0.624, t=c(0.073, 0.923), cn=cn  )
tcs<- scaleReadCounts( tc , ePP )

## End(Not run)

mathieu-lemire/celluloid_0.11 documentation built on May 31, 2018, 7:22 p.m.