Changed default of min.ratio to cleaner -8.

lima1 · Apr 1, 2024 · 5ec2226 · 5ec2226
1 parent daf175b
commit 5ec2226
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/R/adjustLogRatio.R b/R/adjustLogRatio.R
@@ -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)

diff --git a/man/adjustLogRatio.Rd b/man/adjustLogRatio.Rd
diff --git a/tests/testthat/test_adjustLogRatio.R b/tests/testthat/test_adjustLogRatio.R
@@ -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)  
 })