inst/example/shearwater-example.R

In gerstung-lab/deepSNV: Detection of subclonal SNVs in deep sequencing data.

## Load data from deepSNV example
regions <- GRanges("B.FR.83.HXB2_LAI_IIIB_BRU_K034", IRanges(start = 3120, end=3140))
files <- c(system.file("extdata", "test.bam", package="deepSNV"), system.file("extdata", "control.bam", package="deepSNV"))
counts <- loadAllData(files, regions, q=10)

## Run (bbb) computes the Bayes factor
bf <- bbb(counts, model = "OR", rho=1e-4)
vcf <- bf2Vcf(bf, counts, regions, samples = files, prior = 0.5, mvcf = TRUE) 

## Compare to deepSNV
bf <- bbb(counts, model = "AND", rho=1e-4)
dpSNV <- deepSNV(test = files[1], control = files[2], regions=regions, q=10)
plot(p.val(dpSNV), bf[1,,]/(1+bf[1,,]), log="xy")