@@ -30,7 +30,7 @@

 #' log.ratio.adjusted <- adjustLogRatio(log.ratio, 0.65, 1.73)

 #' 

 #' @export adjustLogRatio

-adjustLogRatio <- function(ratio, purity, ploidy, is.log2 = TRUE, min.ratio = 0.004) {

+adjustLogRatio <- function(ratio, purity, ploidy, is.log2 = TRUE, min.ratio = 2^-8) {

     if (is.log2) ratio <- 2^ratio

     adjusted <- (purity * ploidy * ratio + 2 * (1 - purity) * ratio - 2 * (1 - purity)) / (purity * ploidy)

     adjusted <- pmax(min.ratio, adjusted)

@@ -4,7 +4,7 @@

 \alias{adjustLogRatio}

 \title{Adjust tumor vs. normal coverage log ratio for tumor purity and ploidy}

 \usage{

-adjustLogRatio(ratio, purity, ploidy, is.log2 = TRUE, min.ratio = 0.004)

+adjustLogRatio(ratio, purity, ploidy, is.log2 = TRUE, min.ratio = 2^-8)

 }

 \arguments{

 \item{ratio}{Vector of log2 tumor vs normal coverage ratios.}

@@ -10,7 +10,7 @@ test_that("Function returns expected values for example coverage", {

      p <- 1

      log.ratio.offset <- 0

      opt.C <- (2^(log.ratio.adjusted + log.ratio.offset) *  total.ploidy)/p - ((2 * (1 - p))/p)

-     expect_lt(abs(min(log.ratio.adjusted, na.rm=TRUE) - log2(0.004)), 0.001)

+     expect_lt(abs(min(log.ratio.adjusted, na.rm=TRUE) + 8), 0.001)

      expect_lt(median(abs(opt.C - purecn.example.output$results[[1]]$seg$C)), 0.1)  

 })