@@ -11,6 +11,8 @@ BUGFIXES

     o Bugfix #296 was not merged into the developer branch and did not make 

       it into 2.8.0.

+    o Log ratios not shiften to median of sample medians as intended (#356).

+      Thanks @sleyn.  

 Changes in version 2.8.0

@@ -204,17 +204,17 @@ optimal.off.target.counts = 120, plot = FALSE, ...) {

             fcnts_std[, i] <- fcnts_std[,i] / iv

         }

     } else {

-        fcnts_std <- apply(fcnts,2,function(x) x/fcnts_interval_medians)

+        fcnts_std <- apply(fcnts, 2, function(x) x / fcnts_interval_medians)

     }

-    fcnts_interval_non_zero_medians <- apply(fcnts_std, 1, function(x) median(x[x>0]))

-    fcnts_std_imp <- apply(fcnts_std, 2, function(x) { x[x<=0] <- fcnts_interval_non_zero_medians[x<=0]; x})

-    p=0.001

-    li <- quantile(as.vector(fcnts_std_imp), probs= c(p, 1-p))

+    fcnts_interval_non_zero_medians <- apply(fcnts_std, 1, function(x) median(x[x > 0]))

+    fcnts_std_imp <- apply(fcnts_std, 2, function(x) { x[x <= 0] <- fcnts_interval_non_zero_medians[x <= 0]; x})

+    p <- 0.001

+    li <- quantile(as.vector(fcnts_std_imp), probs = c(p, 1 - p))

     fcnts_std_trunc <- fcnts_std_imp

     fcnts_std_trunc[fcnts_std_imp < li[1]] <- li[1]

     fcnts_std_trunc[fcnts_std_imp > li[2]] <- li[2]

     fcnts_std_final <- apply(fcnts_std_trunc, 2, function(x) log2(x / median(x)))

-    fcnts_std_final - median(apply(fcnts_std_final,2,median))

+    fcnts_std_final <- fcnts_std_final - median(apply(fcnts_std_final, 2, median))

     s <- svd(fcnts_std_final)

     ret <- list(