@@ -2,8 +2,8 @@ Package: PureCN

 Type: Package

 Title: Copy number calling and SNV classification using

     targeted short read sequencing

-Version: 1.9.1

-Date: 2017-10-22

+Version: 1.9.2

+Date: 2017-11-05

 Authors@R: c(person("Markus", "Riester", role=c("aut", "cre"),

         email="[email protected]"),

     person("Angad P.", "Singh", role="aut"))

@@ -112,6 +112,7 @@ importFrom(graphics,text)

 importFrom(rtracklayer,import)

 importFrom(stats,C)

 importFrom(stats,aggregate)

+importFrom(stats,binom.test)

 importFrom(stats,complete.cases)

 importFrom(stats,cutree)

 importFrom(stats,dbeta)

@@ -126,7 +127,6 @@ importFrom(stats,loess)

 importFrom(stats,pbeta)

 importFrom(stats,prcomp)

 importFrom(stats,predict)

-importFrom(stats,qpois)

 importFrom(stats,runif)

 importFrom(stats,t.test)

 importFrom(stats,weighted.mean)

@@ -1,3 +1,13 @@

+Changes in version 1.10.0

+------------------------

+

+NEW FEATURES

+

+    o More accurate confidence intervals in callMutationBurden

+

+

+    

+

 Changes in version 1.8.0

 ------------------------

@@ -50,7 +50,7 @@

 #'     callable=callableBed, exclude=exclude, fun.countMutation=myVcfFilter)

 #' 

 #' @export callMutationBurden

-#' @importFrom stats qpois

+#' @importFrom stats binom.test

 callMutationBurden <- function(res, id = 1, remove.flagged = TRUE, 

     min.prior.somatic=0.1, min.cellfraction=0, 

     fun.countMutation=function(vcf) width(vcf)==1,

@@ -121,18 +121,22 @@ callMutationBurden <- function(res, id = 1, remove.flagged = TRUE,

     )

     if (!is.na(ret$callable.bases.ontarget) && ret$callable.bases.ontarget > 0) {

-        lambda <- max(1, ret$somatic.ontarget)

         delta <- ret$callable.bases.ontarget/1e+6

+        ci <- binom.test(x = ret$somatic.ontarget, 

+            n = ret$callable.bases.ontarget)$conf.int

         ret <- cbind(ret, data.frame(

-            somatic.rate.ontarget=ret$somatic.ontarget/delta,

-            somatic.rate.ontarget.95.lower=qpois(0.025, lambda=lambda)/delta,

-            somatic.rate.ontarget.95.upper=qpois(0.975, lambda=lambda)/delta

+            somatic.rate.ontarget = ret$somatic.ontarget/delta,

+            somatic.rate.ontarget.95.lower = ci[1] * 1e+6,

+            somatic.rate.ontarget.95.upper = ci[2] * 1e+6

         ))

-        lambda <- max(1, ret$private.germline.ontarget)

+        # if multiple CI methods were provided, then ret contains multiple rows

+        # now

+        ci <- binom.test(x = ret$private.germline.ontarget, 

+            n = ret$callable.bases.ontarget)$conf.int

         ret <- cbind(ret, data.frame(

-            private.germline.rate.ontarget=ret$private.germline.ontarget/delta,

-            private.germline.rate.ontarget.95.lower=qpois(0.025, lambda=lambda)/delta,

-            private.germline.rate.ontarget.95.upper=qpois(0.975, lambda=lambda)/delta

+            private.germline.rate.ontarget = ret$private.germline.ontarget/delta,

+            private.germline.rate.ontarget.95.lower = ci[1] * 1e+6,

+            private.germline.rate.ontarget.95.upper = ci[2] * 1e+6

         ))

     }