somaticRatio: Estimate somatic ratio for given segments.

In SomatiCA: SomatiCA: identifying, characterizing, and quantifying somatic copy number aberrations from cancer genome sequencing

Description

Somatic ratio is defined as the ratio of read depths between a tumor and its paired normal sample for a given segment. SomatiCA implements different methods to estimate somatic ratio.

Usage

somaticRatio(seg, data, method = "mle", adjust=FALSE)

Arguments

seg	A GRanges object, segments from larsCBSsegment().
data	Input data, from SomatiCAFormat().
method	Method used to estimate somatic ratio of given segments. For the "mle" method somatic ratio is estimated by a maximum likelihood approach. For the "mean" method, somatic ratio is estimated by the ratio between mean of tumor sample and normal sample. For the "geometric", somatic ratio is estimated by geometric mean of somatic ratios of all sites in a given segment.
adjust	Adjust the normal and tumor library and make their median equal.

Value

A GRanges object, segments with annotation of estimated somatic ratio.

Author(s)

Mengjie Chen

See Also

See Also larsCBSsegment.

Examples

chr <- c("chr1", "chr1", "chr1", "chr2", "chr2", "chr2")
start <- c(1, 300, 600, 1, 200, 400) 
end <- c(300, 600, 800, 200, 400, 650)
medLAF <- c(0.2, 0.4, 0.3, 0.2, 0.3, 0.4)
gLAF <- rep(0.4, 6)
seg <- GRanges(seqnames=chr, 
                   ranges=IRanges(start=start, end=end), 
                   medLAF=medLAF, 
                   medgLAF=gLAF) 


rawLAF <- c(rnorm(300, 0.2, 0.05), rnorm(300, 0.4, 0.05), rnorm(200, 0.3, 0.05), 
            rnorm(200, 0.2, 0.05), rnorm(200, 0.3, 0.05), rnorm(250, 0.4, 0.05)) 
germLAF <- c(rnorm(800+650, 0.4, 0.05)) 
reads1 <- c(rpois(300, 25), rpois(300, 50), rpois(200, 60),  rpois(200, 25), 
            rpois(200, 40), rpois(250, 50))
reads2 <- rpois(800+650,50)
chr <- c(rep("chr1", 800), rep("chr2", 650))
position <- c(c(1:800), c(1:650))
zygo <- rep("het", 800+650)
data <- GRanges(seqnames=chr, 
                 ranges=IRanges(start=position, width=1), 
                 zygosity=zygo, 
                 tCount=reads1, 
                 LAF=rawLAF, 
                 tCountN=reads2, 
                 germLAF=germLAF) 
                 
x <- somaticRatio(seg, data, method = "mle")

SomatiCA documentation built on Oct. 5, 2016, 4:18 a.m.