diff --git a/ASCAT-manual.pdf b/ASCAT-manual.pdf
new file mode 100644
index 0000000..526b119
Binary files /dev/null and b/ASCAT-manual.pdf differ
diff --git a/ASCAT/DESCRIPTION b/ASCAT/DESCRIPTION
index 0aff85b..2fd59a4 100644
--- a/ASCAT/DESCRIPTION
+++ b/ASCAT/DESCRIPTION
@@ -15,7 +15,11 @@ Description: R package of ASCAT as published in http://www.ncbi.nlm.nih.gov/
     pubmed/20837533
 Depends:
     R (>= 2.13.0),
-    RColorBrewer
+    RColorBrewer,
+    grDevices,
+    graphics,
+    stats,
+    utils
 License: GPL-3
 LazyLoad: yes
 RoxygenNote: 5.0.1
diff --git a/ASCAT/NAMESPACE b/ASCAT/NAMESPACE
index 2f64bcc..b52f06c 100644
--- a/ASCAT/NAMESPACE
+++ b/ASCAT/NAMESPACE
@@ -15,3 +15,10 @@ export(base.gw.plot)
 export(make_segments)
 export(runASCAT)
 import(RColorBrewer)
+importFrom("grDevices", "adjustcolor", "colorRampPalette", "dev.new",
+             "dev.off", "pdf", "png")
+importFrom("graphics", "abline", "axis", "image", "par", "plot",
+             "points", "rect", "text")
+importFrom("stats", "complete.cases", "cor", "lm", "mad", "median",
+             "na.omit", "runmed", "var")
+importFrom("utils", "read.table", "write.table")
diff --git a/ASCAT/man/ascat.aspcf.Rd b/ASCAT/man/ascat.aspcf.Rd
index 7f3181c..f106a37 100644
--- a/ASCAT/man/ascat.aspcf.Rd
+++ b/ASCAT/man/ascat.aspcf.Rd
@@ -33,8 +33,6 @@ run ASPCF segmentation
 }
 \details{
 This function can be easily parallelised by controlling the selectsamples parameter\cr
-it saves the results in LogR_PCFed[sample]_[segment].txt and BAF_PCFed[sample]_[segment].txt;
-if these files exist, the results are read from them.\cr
-Hence, after parallelisation, copy all the files into the current directory, and run this function to read in the results
+it saves the results in LogR_PCFed[sample]_[segment].txt and BAF_PCFed[sample]_[segment].txt
 }
 
diff --git a/ASCAT/man/ascat.runAscat.Rd b/ASCAT/man/ascat.runAscat.Rd
index 516e8ab..9080bbf 100644
--- a/ASCAT/man/ascat.runAscat.Rd
+++ b/ASCAT/man/ascat.runAscat.Rd
@@ -32,6 +32,7 @@ an ASCAT output object, containing:\cr
 6. nonaberrantarrays: arrays on which ASCAT analysis indicates that they show virtually no aberrations\cr
 7. segments: an array containing the copy number segments of each sample (not including failed arrays)\cr
 8. segments_raw: an array containing the copy number segments of each sample without any rounding applied\cr
+9. distance_matrix: distances for a range of ploidy and tumor percentage values
 }
 \description{
 ASCAT main function, calculating the allele-specific copy numbers
diff --git a/ASCAT/man/runASCAT.Rd b/ASCAT/man/runASCAT.Rd
index 9b31b1c..5d87a72 100644
--- a/ASCAT/man/runASCAT.Rd
+++ b/ASCAT/man/runASCAT.Rd
@@ -37,7 +37,7 @@ runASCAT(lrr, baf, lrrsegmented, bafsegmented, gender, SNPpos, chromosomes,
 
 \item{nonroundedprofilepng}{if NA: copy number profile before rounding is plotted (total copy number as well as the copy number of the minor allele), if filename is given, the plot is written to a .png file}
 
-\item{aberrationreliabilitypng}{if NA: aberration reliability score is plotted, if filename is given, the plot is written to a .png file}
+\item{aberrationreliabilitypng}{aberration reliability score is plotted if filename is given}
 
 \item{gamma}{technology parameter, compaction of Log R profiles (expected decrease in case of deletion in diploid sample, 100\% aberrant cells; 1 in ideal case, 0.55 of Illumina 109K arrays)}