diff --git a/DESCRIPTION b/DESCRIPTION
index 5e9d4a6..32099bb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CNVMetrics
 Type: Package
-Version: 0.1.1
-Date: 2021-01-29
+Version: 0.1.2
+Date: 2021-02-10
 Title: Copy Number Variant Metrics
 Description: Calculate similarity metrics to facilite copy number variant 
     comparison among samples and/or methods.
diff --git a/NAMESPACE b/NAMESPACE
index a34436f..c5c4850 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -2,7 +2,7 @@
 
 S3method(is,CNVMetric)
 S3method(print,CNVMetric)
-export(calculateOverlapRegionsMetric)
+export(calculateOverlapMetric)
 export(calculateWeightedEuclideanDistance)
 export(plotOverlapMetric)
 export(prepareInformation)
diff --git a/NEWS.md b/NEWS.md
index 5ff92b0..247af18 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,9 +1,21 @@
+# CNVMetrics 0.1.2
+
+NEW FEATURES
+
+* Added a `NEWS.md` file to track changes to the package.
+* `plotOneOverlapMetric()` method enables plotting result of overlapping metric calculation.
+
+SIGNIFICANT USER-VISIBLE CHANGES
+
+* `calculateOverlapRegionsMetric()` method changed to `calculateOverlapMetric()`.
+
+
 # CNVMetrics 0.1.1
 
 NEW FEATURES
 
 * Added a `NEWS.md` file to track changes to the package.
-* `calculateOverlapRegionsMetric()` enables calculation of similarity metrics using overlapping amplified/deleted regions.
+* `calculateOverlapRegionsMetric()` method enables calculation of similarity metrics using overlapping amplified/deleted regions.
 
 SIGNIFICANT USER-VISIBLE CHANGES
 
diff --git a/R/CNVMetrics.R b/R/CNVMetrics.R
index fd14bf7..0f53395 100644
--- a/R/CNVMetrics.R
+++ b/R/CNVMetrics.R
@@ -15,5 +15,6 @@
 #' Maintainer:
 #' Astrid Deschênes <adeschen@hotmail.com>
 #'
+#' @encoding UTF-8
 #' @keywords package
 NULL
diff --git a/R/CNVMetricsOverlapInternalMethods.R b/R/CNVMetricsOverlapInternalMethods.R
index 231af61..eaca640 100644
--- a/R/CNVMetricsOverlapInternalMethods.R
+++ b/R/CNVMetricsOverlapInternalMethods.R
@@ -68,27 +68,27 @@
 #'     state = c("AMPLIFICATION", "DELETION", "DELETION"))
 #' 
 #' ## Calculate Sorensen metric for the amplified regions   
-#' CNVMetrics:::calculateOverlapMetric(sample01, sample02, method="sorensen",
-#'     type="AMPLIFICATION")
+#' CNVMetrics:::calculateOneOverlapMetric(sample01, sample02, 
+#'     method="sorensen", type="AMPLIFICATION")
 #' 
 #' ## Calculate Szymkiewicz-Simpson metric for the amplified regions   
 #' ## Amplified regions of sample02 are a subset of the amplified 
 #' ## regions in sample01
-#' CNVMetrics:::calculateOverlapMetric(sample01, sample02, method="szymkiewicz",
-#'     type="AMPLIFICATION")
+#' CNVMetrics:::calculateOneOverlapMetric(sample01, sample02, 
+#'     method="szymkiewicz", type="AMPLIFICATION")
 #' 
 #' ## Calculate Sorensen metric for the deleted regions   
-#' CNVMetrics:::calculateOverlapMetric(sample01, sample02, method="sorensen",
-#'     type="DELETION")
+#' CNVMetrics:::calculateOneOverlapMetric(sample01, sample02, 
+#'     method="sorensen", type="DELETION")
 #'     
 #' ## Calculate Szymkiewicz-Simpson metric for the deleted regions    
-#' CNVMetrics:::calculateOverlapMetric(sample01, sample02, method="szymkiewicz",
-#'     type="DELETION")
+#' CNVMetrics:::calculateOneOverlapMetric(sample01, sample02,
+#'     method="szymkiewicz", type="DELETION")
 #' 
 #' @author Astrid Deschênes
 #' @encoding UTF-8
 #' @keywords internal
-calculateOverlapMetric <- function(sample01, sample02, method, type) {
+calculateOneOverlapMetric <- function(sample01, sample02, method, type) {
     
     sample01 <- sample01[sample01$state == type,]
     sample02 <- sample02[sample02$state == type,]
@@ -246,7 +246,7 @@ calculateSzymkiewicz <- function(sample01, sample02) {
 #' amplified/deleted regions. 
 #' 
 #' @param metric a \code{CNVMetric} object containing the metrics calculated
-#' by \code{calculateOverlapRegionsMetric}.
+#' by \code{calculateOverlapMetric}.
 #' 
 #' @param type a \code{character} string indicating which graph to generate. 
 #' This should be (an unambiguous abbreviation of) one of  
@@ -291,7 +291,7 @@ calculateSzymkiewicz <- function(sample01, sample02) {
 #'     state = c("AMPLIFICATION", "DELETION"))
 #' 
 #' ## Calculating Sorensen metric
-#' metric <- calculateOverlapRegionsMetric(demo, method="sorensen")
+#' metric <- calculateOverlapMetric(demo, method="sorensen")
 #' 
 #' ## Plot both amplification metrics using darkorange color
 #' CNVMetrics:::plotOneOverlapMetric(metric, type="AMPLIFICATION", 
@@ -314,8 +314,8 @@ plotOneOverlapMetric <- function(metric, type, colorRange, show_colnames, ...)
 
     ## Prepare main title (might not be used if main argument given by user)
     metricInfo <- switch(attributes(metric)$metric, 
-                         "szymkiewicz"="Szymkiewicz-Simpson", 
-                         "sorensen"="Sorensen")
+                            "szymkiewicz"="Szymkiewicz-Simpson", 
+                            "sorensen"="Sorensen")
     metricInfo <- paste0(type, " - ", metricInfo, " metric")
     
     ## Create heatmap
@@ -328,10 +328,10 @@ plotOneOverlapMetric <- function(metric, type, colorRange, show_colnames, ...)
         
         if (!hasArg("main")) {
             pheatmap(metricMat, main=metricInfo, show_colnames=show_colnames, 
-                     color=colors, breaks=breaks, ...)[[4]] 
+                        color=colors, breaks=breaks, ...)[[4]] 
         } else {
             pheatmap(metricMat, show_colnames=show_colnames, 
-                     color=colors, breaks=breaks, ...)[[4]]  
+                        color=colors, breaks=breaks, ...)[[4]]  
         }
     } else {
         if (!hasArg("main")) {
diff --git a/R/CNVMetricsOverlapMethods.R b/R/CNVMetricsOverlapMethods.R
index 2fb26c2..ff68049 100644
--- a/R/CNVMetricsOverlapMethods.R
+++ b/R/CNVMetricsOverlapMethods.R
@@ -102,16 +102,16 @@
 #'     state = c("AMPLIFICATION", "DELETION"))
 #' 
 #' ## Calculating Sorensen metric
-#' calculateOverlapRegionsMetric(demo, method="sorensen")
+#' calculateOverlapMetric(demo, method="sorensen")
 #' 
 #' ## Calculating Szymkiewicz-Simpson metric
-#' calculateOverlapRegionsMetric(demo, method="szymkiewicz")
+#' calculateOverlapMetric(demo, method="szymkiewicz")
 #' 
 #' @author Astrid Deschênes, Pascal Belleau
 #' @import GenomicRanges 
 #' @encoding UTF-8
 #' @export
-calculateOverlapRegionsMetric <- function(segmentData, 
+calculateOverlapMetric <- function(segmentData, 
                                     method=c("sorensen", "szymkiewicz")) {
     
     method <- match.arg(method)
@@ -143,7 +143,7 @@ calculateOverlapRegionsMetric <- function(segmentData,
         
         for(i in seq_len(nb)[-1]) {
             for(j in seq_len(i-1)) {
-                dataTMP[i, j] <- calculateOverlapMetric(
+                dataTMP[i, j] <- calculateOneOverlapMetric(
                     sample01=segmentData[[names[i]]], 
                     sample02=segmentData[[names[j]]],
                     method=method, type=type)
@@ -169,7 +169,7 @@ calculateOverlapRegionsMetric <- function(segmentData,
 #' heatmap related to amplified, deleted regions or both.
 #' 
 #' @param metric a \code{CNVMetric} object containing the metrics calculated
-#' by \code{calculateOverlapRegionsMetric}.
+#' by \code{calculateOverlapMetric}.
 #' 
 #' @param type a \code{character} string indicating which graph to generate. 
 #' This should be (an unambiguous abbreviation of) one of "\code{BOTH}", 
@@ -215,7 +215,7 @@ calculateOverlapRegionsMetric <- function(segmentData,
 #'     state = c("AMPLIFICATION", "DELETION"))
 #' 
 #' ## Calculating Sorensen metric
-#' metric <- calculateOverlapRegionsMetric(demo, method="sorensen")
+#' metric <- calculateOverlapMetric(demo, method="sorensen")
 #' 
 #' ## Plot both amplification and deletion metrics
 #' plotOverlapMetric(metric, type="BOTH")
diff --git a/man/CNVMetrics-package.Rd b/man/CNVMetrics-package.Rd
index b416b75..fa45bbd 100644
--- a/man/CNVMetrics-package.Rd
+++ b/man/CNVMetrics-package.Rd
@@ -1,6 +1,7 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/CNVMetrics.R
 \docType{package}
+\encoding{UTF-8}
 \name{CNVMetrics-package}
 \alias{CNVMetrics-package}
 \alias{CNVMetrics}
diff --git a/man/calculateOneOverlapMetric.Rd b/man/calculateOneOverlapMetric.Rd
new file mode 100644
index 0000000..58f824b
--- /dev/null
+++ b/man/calculateOneOverlapMetric.Rd
@@ -0,0 +1,101 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CNVMetricsOverlapInternalMethods.R
+\encoding{UTF-8}
+\name{calculateOneOverlapMetric}
+\alias{calculateOneOverlapMetric}
+\title{Calculate metric using overlapping amplified/deleted regions between 
+two samples.}
+\usage{
+calculateOneOverlapMetric(sample01, sample02, method, type)
+}
+\arguments{
+\item{sample01}{a \code{GRanges} which contains a collection of 
+genomic ranges representing copy number events for the first sample. 
+The \code{GRanges} must have a metadata column called '\code{state}' with 
+amplified regions identified as '\code{AMPLIFICATION}' and 
+deleted regions identified as '\code{DELETION}'; regions with different 
+identifications will not be used in the
+calculation of the metric.}
+
+\item{sample02}{a \code{GRanges} which contains a collection of 
+genomic ranges representing copy number events for the second sample.}
+
+\item{method}{a \code{character} string representing the metric to be
+used ('\code{sorensen}' or '\code{szymkiewicz}'.}
+
+\item{type}{a \code{character} string representing the type of 
+copy number events to be used ('\code{AMPLIFICATION}' or '\code{DELETION}').}
+}
+\value{
+a \code{numeric}, the value of the specified metric. If
+the metric cannot be calculated, \code{NA} is returned.
+}
+\description{
+Calculate a specific metric using overlapping 
+amplified/deleted regions between two samples.
+}
+\details{
+The method calculates a specified metric using overlapping
+regions between the samples. Only regions corresponding to the type
+specified by user are used in the calculation of the metric. The strand of 
+the regions is not taken into account while
+calculating the metric.
+
+The Sorensen metric is calculated by dividing twice the size of 
+the intersection by the sum of the size of the two sets. If the sum of
+the size of the two sets is zero; the value \code{NA} is
+returned instead. 
+
+The Szymkiewicz-Simpson metric is calculated by dividing the size of 
+the intersection by the smaller of the size of the two sets. If one sample
+has a size of zero, the metric is not calculated; the value \code{NA} is
+returned instead.
+}
+\examples{
+
+## Load required package to generate the two samples
+require(GenomicRanges)
+
+## Generate two samples with identical sequence levels
+sample01 <- GRanges(seqnames = "chr1", 
+    ranges =  IRanges(start = c(100, 201, 400), 
+    end = c(200, 350, 500)), strand =  "*",
+    state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
+sample02 <- GRanges(seqnames = "chr1", 
+    ranges =  IRanges(start = c(150, 200, 450), 
+    end = c(250, 350, 500)), strand =  "*",
+    state = c("AMPLIFICATION", "DELETION", "DELETION"))
+
+## Calculate Sorensen metric for the amplified regions   
+CNVMetrics:::calculateOneOverlapMetric(sample01, sample02, 
+    method="sorensen", type="AMPLIFICATION")
+
+## Calculate Szymkiewicz-Simpson metric for the amplified regions   
+## Amplified regions of sample02 are a subset of the amplified 
+## regions in sample01
+CNVMetrics:::calculateOneOverlapMetric(sample01, sample02, 
+    method="szymkiewicz", type="AMPLIFICATION")
+
+## Calculate Sorensen metric for the deleted regions   
+CNVMetrics:::calculateOneOverlapMetric(sample01, sample02, 
+    method="sorensen", type="DELETION")
+    
+## Calculate Szymkiewicz-Simpson metric for the deleted regions    
+CNVMetrics:::calculateOneOverlapMetric(sample01, sample02,
+    method="szymkiewicz", type="DELETION")
+
+}
+\references{
+Sørensen, Thorvald. n.d. “A Method of Establishing Groups of Equal 
+Amplitude in Plant Sociology Based on Similarity of Species and Its 
+Application to Analyses of the Vegetation on Danish Commons.” 
+Biologiske Skrifter, no. 5: 1–34.
+
+Vijaymeena, M. K, and Kavitha K. 2016. “A Survey on Similarity Measures in 
+Text Mining.” Machine Learning and Applications: An International 
+Journal 3 (1): 19–28. doi: \url{https://doi.org/10.5121/mlaij.2016.3103}
+}
+\author{
+Astrid Deschênes
+}
+\keyword{internal}
diff --git a/man/calculateOverlapMetric.Rd b/man/calculateOverlapMetric.Rd
index 49b561d..a41548d 100644
--- a/man/calculateOverlapMetric.Rd
+++ b/man/calculateOverlapMetric.Rd
@@ -1,88 +1,106 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CNVMetricsOverlapInternalMethods.R
+% Please edit documentation in R/CNVMetricsOverlapMethods.R
 \encoding{UTF-8}
 \name{calculateOverlapMetric}
 \alias{calculateOverlapMetric}
-\title{Calculate metric using overlapping amplified/deleted regions between 
-two samples.}
+\title{Calculate metric using overlapping amplified/deleted regions}
 \usage{
-calculateOverlapMetric(sample01, sample02, method, type)
+calculateOverlapMetric(segmentData, method = c("sorensen", "szymkiewicz"))
 }
 \arguments{
-\item{sample01}{a \code{GRanges} which contains a collection of 
-genomic ranges representing copy number events for the first sample. 
-The \code{GRanges} must have a metadata column called '\code{state}' with 
-amplified regions identified as '\code{AMPLIFICATION}' and 
-deleted regions identified as '\code{DELETION}'; regions with different 
-identifications will not be used in the
+\item{segmentData}{a \code{GRangesList} that contains a collection of 
+genomic ranges representing copy number events, including amplified/deleted 
+status, from at least 2 samples. All samples must have a metadata column 
+called '\code{state}' with amplified regions identified as 
+'\code{AMPLIFICATION}' and deleted regions identified as '\code{DELETION}'; 
+regions with different identifications will not be used in the
 calculation of the metric.}
 
-\item{sample02}{a \code{GRanges} which contains a collection of 
-genomic ranges representing copy number events for the second sample.}
-
-\item{method}{a \code{character} string representing the metric to be
-used ('\code{sorensen}' or '\code{szymkiewicz}'.}
-
-\item{type}{a \code{character} string representing the type of 
-copy number events to be used ('\code{AMPLIFICATION}' or '\code{DELETION}').}
+\item{method}{a \code{character} string representing the metric to be used. 
+This should be (an unambiguous abbreviation of) one of "sorensen" or 
+"szymkiewicz". Default: "sorensen".}
 }
 \value{
-a \code{numeric}, the value of the specified metric. If
-the metric cannot be calculated, \code{NA} is returned.
+a \code{list} of class "\code{CNVMetric}". This list has
+the following components:
+\itemize{
+\item{\code{AMPLIFICATION}}{ a lower-triangular \code{matrix} with the 
+    results of the selected metric on the amplified regions for each paired
+    samples. The value \code{NA} is present when the metric cannot be 
+    calculated. The value \code{NA} is also present in the top-triangular 
+    section of the matrix.
+ }
+ \item{\code{DELETION}}{ a lower-triangular \code{matrix} with the 
+    results of the selected metric on the deleted regions for each paired
+    samples. The value \code{NA} is present when the metric cannot be 
+    calculated. The value \code{NA} is also present in the top-triangular 
+    section of the matrix.
+}}
+
+The object has the following attributes (besides "class" equal 
+to "CNVMetric"):
+\itemize{
+\item{\code{metric}}{ the metric used for the calculation.
+ } 
+\item{\code{names}}{ the names of the two matrix containing the metrics for
+the amplified and deleted regions.
+}}
 }
 \description{
 Calculate a specific metric using overlapping 
-amplified/deleted regions between two samples.
+amplified/deleted regions between to samples. The metric is calculated for
+the amplified and deleted regions separately. When more than 2 samples are 
+present, the metric is calculated for each sample pair.
 }
 \details{
-The method calculates a specified metric using overlapping
-regions between the samples. Only regions corresponding to the type
-specified by user are used in the calculation of the metric. The strand of 
-the regions is not taken into account while
-calculating the metric.
+The two methods each estimate the overlap between paired samples. They use 
+different metrics, all in the range [0, 1] with 0 indicating no overlap.
+
+The available metrics are (written for two GRanges):
 
-The Sorensen metric is calculated by dividing twice the size of 
-the intersection by the sum of the size of the two sets. If the sum of
-the size of the two sets is zero; the value \code{NA} is
-returned instead. 
+\code{sorensen}:
 
-The Szymkiewicz-Simpson metric is calculated by dividing the size of 
-the intersection by the smaller of the size of the two sets. If one sample
-has a size of zero, the metric is not calculated; the value \code{NA} is
-returned instead.
+This metric is calculated by dividing twice the size of the intersection 
+by the sum of the size of the two sets. 
+With this metric, an overlap metric value of 1 is only obtained when the
+two samples are identical. 
+
+\code{szymkiewicz}:
+
+This metric is calculated by dividing the size of the intersection 
+by the size of the smallest set. With this metric, if one set is a 
+subset of the other set, the overlap metric value is 1.
 }
 \examples{
 
-## Load required package to generate the two samples
+## Load required package to generate the samples
 require(GenomicRanges)
 
-## Generate two samples with identical sequence levels
-sample01 <- GRanges(seqnames = "chr1", 
-    ranges =  IRanges(start = c(100, 201, 400), 
-    end = c(200, 350, 500)), strand =  "*",
+## Create a GRangesList object with 3 samples
+## The stand of the regions doesn't affect the calculation of the metric
+demo <- GRangesList()
+demo[["sample01"]] <- GRanges(seqnames = "chr1", 
+    ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
+    end = c(2004603, 4577608, 31695808)), strand =  "*",
+    state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
+
+demo[["sample02"]] <- GRanges(seqnames = "chr1", 
+    ranges =  IRanges(start = c(1995066, 31611222, 31690000), 
+    end = c(2204505, 31689898, 31895666)), strand =  c("-", "+", "+"),
     state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
-sample02 <- GRanges(seqnames = "chr1", 
-    ranges =  IRanges(start = c(150, 200, 450), 
-    end = c(250, 350, 500)), strand =  "*",
-    state = c("AMPLIFICATION", "DELETION", "DELETION"))
 
-## Calculate Sorensen metric for the amplified regions   
-CNVMetrics:::calculateOverlapMetric(sample01, sample02, method="sorensen",
-    type="AMPLIFICATION")
+## The amplified region in sample03 is a subset of the amplified regions 
+## in sample01
+demo[["sample03"]] <- GRanges(seqnames = "chr1", 
+    ranges =  IRanges(start = c(1906069, 4558838), 
+    end = c(1909505, 4570601)), strand =  "*",
+    state = c("AMPLIFICATION", "DELETION"))
 
-## Calculate Szymkiewicz-Simpson metric for the amplified regions   
-## Amplified regions of sample02 are a subset of the amplified 
-## regions in sample01
-CNVMetrics:::calculateOverlapMetric(sample01, sample02, method="szymkiewicz",
-    type="AMPLIFICATION")
+## Calculating Sorensen metric
+calculateOverlapMetric(demo, method="sorensen")
 
-## Calculate Sorensen metric for the deleted regions   
-CNVMetrics:::calculateOverlapMetric(sample01, sample02, method="sorensen",
-    type="DELETION")
-    
-## Calculate Szymkiewicz-Simpson metric for the deleted regions    
-CNVMetrics:::calculateOverlapMetric(sample01, sample02, method="szymkiewicz",
-    type="DELETION")
+## Calculating Szymkiewicz-Simpson metric
+calculateOverlapMetric(demo, method="szymkiewicz")
 
 }
 \references{
@@ -96,6 +114,5 @@ Text Mining.” Machine Learning and Applications: An International
 Journal 3 (1): 19–28. doi: \url{https://doi.org/10.5121/mlaij.2016.3103}
 }
 \author{
-Astrid Deschênes
+Astrid Deschênes, Pascal Belleau
 }
-\keyword{internal}
diff --git a/man/calculateOverlapRegionsMetric.Rd b/man/calculateOverlapRegionsMetric.Rd
deleted file mode 100644
index 019bed4..0000000
--- a/man/calculateOverlapRegionsMetric.Rd
+++ /dev/null
@@ -1,121 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/CNVMetricsOverlapMethods.R
-\encoding{UTF-8}
-\name{calculateOverlapRegionsMetric}
-\alias{calculateOverlapRegionsMetric}
-\title{Calculate metric using overlapping amplified/deleted regions}
-\usage{
-calculateOverlapRegionsMetric(
-  segmentData,
-  method = c("sorensen", "szymkiewicz")
-)
-}
-\arguments{
-\item{segmentData}{a \code{GRangesList} that contains a collection of 
-genomic ranges representing copy number events, including amplified/deleted 
-status, from at least 2 samples. All samples must have a metadata column 
-called '\code{state}' with amplified regions identified as 
-'\code{AMPLIFICATION}' and deleted regions identified as '\code{DELETION}'; 
-regions with different identifications will not be used in the
-calculation of the metric.}
-
-\item{method}{a \code{character} string representing the metric to be used. 
-This should be (an unambiguous abbreviation of) one of "sorensen" or 
-"szymkiewicz". Default: "sorensen".}
-}
-\value{
-a \code{list} of class "\code{CNVMetric}". This list has
-the following components:
-\itemize{
-\item{\code{AMPLIFICATION}}{ a lower-triangular \code{matrix} with the 
-    results of the selected metric on the amplified regions for each paired
-    samples. The value \code{NA} is present when the metric cannot be 
-    calculated. The value \code{NA} is also present in the top-triangular 
-    section of the matrix.
- }
- \item{\code{DELETION}}{ a lower-triangular \code{matrix} with the 
-    results of the selected metric on the deleted regions for each paired
-    samples. The value \code{NA} is present when the metric cannot be 
-    calculated. The value \code{NA} is also present in the top-triangular 
-    section of the matrix.
-}}
-
-The object has the following attributes (besides "class" equal 
-to "CNVMetric"):
-\itemize{
-\item{\code{metric}}{ the metric used for the calculation.
- } 
-\item{\code{names}}{ the names of the two matrix containing the metrics for
-the amplified and deleted regions.
-}}
-}
-\description{
-Calculate a specific metric using overlapping 
-amplified/deleted regions between to samples. The metric is calculated for
-the amplified and deleted regions separately. When more than 2 samples are 
-present, the metric is calculated for each sample pair.
-}
-\details{
-The two methods each estimate the overlap between paired samples. They use 
-different metrics, all in the range [0, 1] with 0 indicating no overlap.
-
-The available metrics are (written for two GRanges):
-
-\code{sorensen}:
-
-This metric is calculated by dividing twice the size of the intersection 
-by the sum of the size of the two sets. 
-With this metric, an overlap metric value of 1 is only obtained when the
-two samples are identical. 
-
-\code{szymkiewicz}:
-
-This metric is calculated by dividing the size of the intersection 
-by the size of the smallest set. With this metric, if one set is a 
-subset of the other set, the overlap metric value is 1.
-}
-\examples{
-
-## Load required package to generate the samples
-require(GenomicRanges)
-
-## Create a GRangesList object with 3 samples
-## The stand of the regions doesn't affect the calculation of the metric
-demo <- GRangesList()
-demo[["sample01"]] <- GRanges(seqnames = "chr1", 
-    ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
-    end = c(2004603, 4577608, 31695808)), strand =  "*",
-    state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
-
-demo[["sample02"]] <- GRanges(seqnames = "chr1", 
-    ranges =  IRanges(start = c(1995066, 31611222, 31690000), 
-    end = c(2204505, 31689898, 31895666)), strand =  c("-", "+", "+"),
-    state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
-
-## The amplified region in sample03 is a subset of the amplified regions 
-## in sample01
-demo[["sample03"]] <- GRanges(seqnames = "chr1", 
-    ranges =  IRanges(start = c(1906069, 4558838), 
-    end = c(1909505, 4570601)), strand =  "*",
-    state = c("AMPLIFICATION", "DELETION"))
-
-## Calculating Sorensen metric
-calculateOverlapRegionsMetric(demo, method="sorensen")
-
-## Calculating Szymkiewicz-Simpson metric
-calculateOverlapRegionsMetric(demo, method="szymkiewicz")
-
-}
-\references{
-Sørensen, Thorvald. n.d. “A Method of Establishing Groups of Equal 
-Amplitude in Plant Sociology Based on Similarity of Species and Its 
-Application to Analyses of the Vegetation on Danish Commons.” 
-Biologiske Skrifter, no. 5: 1–34.
-
-Vijaymeena, M. K, and Kavitha K. 2016. “A Survey on Similarity Measures in 
-Text Mining.” Machine Learning and Applications: An International 
-Journal 3 (1): 19–28. doi: \url{https://doi.org/10.5121/mlaij.2016.3103}
-}
-\author{
-Astrid Deschênes, Pascal Belleau
-}
diff --git a/man/plotOneOverlapMetric.Rd b/man/plotOneOverlapMetric.Rd
index 5f5f7ec..403a297 100644
--- a/man/plotOneOverlapMetric.Rd
+++ b/man/plotOneOverlapMetric.Rd
@@ -10,7 +10,7 @@ plotOneOverlapMetric(metric, type, colorRange, show_colnames, ...)
 }
 \arguments{
 \item{metric}{a \code{CNVMetric} object containing the metrics calculated
-by \code{calculateOverlapRegionsMetric}.}
+by \code{calculateOverlapMetric}.}
 
 \item{type}{a \code{character} string indicating which graph to generate. 
 This should be (an unambiguous abbreviation of) one of  
@@ -56,7 +56,7 @@ demo[["sample03"]] <- GRanges(seqnames = "chr1",
     state = c("AMPLIFICATION", "DELETION"))
 
 ## Calculating Sorensen metric
-metric <- calculateOverlapRegionsMetric(demo, method="sorensen")
+metric <- calculateOverlapMetric(demo, method="sorensen")
 
 ## Plot both amplification metrics using darkorange color
 CNVMetrics:::plotOneOverlapMetric(metric, type="AMPLIFICATION", 
diff --git a/man/plotOverlapMetric.Rd b/man/plotOverlapMetric.Rd
index fae7bbb..ec2859f 100644
--- a/man/plotOverlapMetric.Rd
+++ b/man/plotOverlapMetric.Rd
@@ -15,7 +15,7 @@ plotOverlapMetric(
 }
 \arguments{
 \item{metric}{a \code{CNVMetric} object containing the metrics calculated
-by \code{calculateOverlapRegionsMetric}.}
+by \code{calculateOverlapMetric}.}
 
 \item{type}{a \code{character} string indicating which graph to generate. 
 This should be (an unambiguous abbreviation of) one of "\code{BOTH}", 
@@ -67,7 +67,7 @@ demo[["sample03"]] <- GRanges(seqnames = "chr1",
     state = c("AMPLIFICATION", "DELETION"))
 
 ## Calculating Sorensen metric
-metric <- calculateOverlapRegionsMetric(demo, method="sorensen")
+metric <- calculateOverlapMetric(demo, method="sorensen")
 
 ## Plot both amplification and deletion metrics
 plotOverlapMetric(metric, type="BOTH")
diff --git a/tests/testthat/test-CNVMetricMethods.R b/tests/testthat/test-CNVMetricMethods.R
index 35bd679..1b8cfd8 100644
--- a/tests/testthat/test-CNVMetricMethods.R
+++ b/tests/testthat/test-CNVMetricMethods.R
@@ -103,57 +103,4 @@ test_that("calculateWeightedEuclideanDistance() must return good results 02", {
 })
 
 
-### Tests calculateOverlapRegionsMetric() results
 
-context("calculateOverlapRegionsMetric() results")
-
-test_that("calculateOverlapRegionsMetric() must return an error when segmentData has only one sample", {
-    
-    error_message <- "at least 2 samples must be present in the segmentData"
-    
-    demo <- GRangesList()
-    demo[["sample01"]] <- GRanges(seqnames = "chr1", 
-        ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
-        end = c(2004603, 4577608, 31695808)), strand =  "*",
-        state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
-    
-    expect_error(calculateOverlapRegionsMetric(demo), error_message) 
-})
-
-test_that("calculateOverlapRegionsMetric() must return an error when segmentData has metadata status instead of state", {
-    
-    error_message <- paste0("at least one sample doesn't have a metadata column ", 
-                                "called \'state\'")
-    
-    demo <- GRangesList()
-    demo[["sample01"]] <- GRanges(seqnames = "chr1", 
-                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
-                                                    end = c(2004603, 4577608, 31695808)), strand =  "*",
-                                  status = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
-    
-    demo[["sample02"]] <- GRanges(seqnames = "chr1", 
-                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
-                                                    end = c(2004603, 4577608, 31695808)), strand =  "*",
-                                  status= c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
-    
-    expect_error(calculateOverlapRegionsMetric(demo), error_message) 
-})
-
-test_that("calculateOverlapRegionsMetric() must return an error when segmentData doesn't have metadata state", {
-    
-    error_message <- paste0("at least one sample doesn't have a metadata column ", 
-                                "called \'state\'")
-    
-    demo <- GRangesList()
-    demo[["sample01"]] <- GRanges(seqnames = "chr1", 
-                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
-                                                    end = c(2004603, 4577608, 31695808)), 
-                                  strand =  "*")
-    
-    demo[["sample02"]] <- GRanges(seqnames = "chr1", 
-                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
-                                                    end = c(2004603, 4577608, 31695808)), 
-                                  strand =  "*")
-    
-    expect_error(calculateOverlapRegionsMetric(demo), error_message) 
-})
diff --git a/tests/testthat/test-CNVMetricsOverlapMethods.R b/tests/testthat/test-CNVMetricsOverlapMethods.R
index c49721b..33256f5 100644
--- a/tests/testthat/test-CNVMetricsOverlapMethods.R
+++ b/tests/testthat/test-CNVMetricsOverlapMethods.R
@@ -7,11 +7,11 @@ library(IRanges)
 library(GenomeInfoDb)
 
 
-### Tests calculateOverlapRegionsMetric() results
+### Tests calculateOverlapMetric() results
 
-context("calculateOverlapRegionsMetric() results")
+context("calculateOverlapMetric() results")
 
-test_that("calculateOverlapRegionsMetric() must return error when only one sample present", {
+test_that("calculateOverlapMetric() must return error when only one sample present", {
     
     demo <- GRangesList()
     demo[["sample01"]] <- GRanges(seqnames = "chr1",
@@ -22,12 +22,12 @@ test_that("calculateOverlapRegionsMetric() must return error when only one sampl
 
     error_message <- "at least 2 samples must be present in the segmentData"
     
-    expect_error(calculateOverlapRegionsMetric(segmentData = demo, 
+    expect_error(calculateOverlapMetric(segmentData = demo, 
                                                 method = "sorensen"), 
                  error_message)
 })
 
-test_that("calculateOverlapRegionsMetric() must return error when method is available", {
+test_that("calculateOverlapMetric() must return error when method is available", {
     
     demo <- GRangesList()
     demo[["sample01"]] <- GRanges(seqnames = "chr1",
@@ -43,13 +43,13 @@ test_that("calculateOverlapRegionsMetric() must return error when method is avai
              paste(dQuote(c("sorensen", "szymkiewicz")), 
                                                 collapse = ", "))
 
-    expect_error(calculateOverlapRegionsMetric(segmentData = demo, 
+    expect_error(calculateOverlapMetric(segmentData = demo, 
                                                method = "typo"), 
                  error_message)
 })
 
 
-test_that("calculateOverlapRegionsMetric() must return 1 when two samples identical with sorensen", {
+test_that("calculateOverlapMetric() must return 1 when two samples identical with sorensen", {
     
     demo <- GRangesList()
     demo[["sample01"]] <- GRanges(seqnames = "chr1",
@@ -61,7 +61,7 @@ test_that("calculateOverlapRegionsMetric() must return 1 when two samples identi
                     end = c(2004603, 4577608, 31695808)), strand =  "*",
                     state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
     
-    result <- calculateOverlapRegionsMetric(segmentData=demo, 
+    result <- calculateOverlapMetric(segmentData=demo, 
                                                 method="sorensen")
     
     expected <- list()
@@ -82,7 +82,7 @@ test_that("calculateOverlapRegionsMetric() must return 1 when two samples identi
 })
 
 
-test_that("calculateOverlapRegionsMetric() must return expected results with sorensen", {
+test_that("calculateOverlapMetric() must return expected results with sorensen", {
     
     demo <- GRangesList()
     demo[["sample01"]] <- GRanges(seqnames = "chr1",
@@ -99,7 +99,7 @@ test_that("calculateOverlapRegionsMetric() must return expected results with sor
                 state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
     
     
-    result <- calculateOverlapRegionsMetric(segmentData=demo, 
+    result <- calculateOverlapMetric(segmentData=demo, 
                                             method="sorensen")
     
     expected <- list()
@@ -123,7 +123,7 @@ test_that("calculateOverlapRegionsMetric() must return expected results with sor
 })
 
 
-test_that("calculateOverlapRegionsMetric() must return expected results with szymkiewicz", {
+test_that("calculateOverlapMetric() must return expected results with szymkiewicz", {
     
     demo <- GRangesList()
     demo[["sample01"]] <- GRanges(seqnames = "chr1",
@@ -139,7 +139,7 @@ test_that("calculateOverlapRegionsMetric() must return expected results with szy
                     end = c(250, 700, 2000)), strand =  "*",
                     state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
     
-    result <- calculateOverlapRegionsMetric(segmentData=demo, 
+    result <- calculateOverlapMetric(segmentData=demo, 
                                             metho="szymkiewicz")
     
     expected <- list()
@@ -163,6 +163,58 @@ test_that("calculateOverlapRegionsMetric() must return expected results with szy
 })
 
 
+test_that("calculateOverlapMetric() must return an error when segmentData has only one sample", {
+    
+    error_message <- "at least 2 samples must be present in the segmentData"
+    
+    demo <- GRangesList()
+    demo[["sample01"]] <- GRanges(seqnames = "chr1", 
+                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
+                                                    end = c(2004603, 4577608, 31695808)), strand =  "*",
+                                  state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
+    
+    expect_error(calculateOverlapMetric(demo), error_message) 
+})
+
+test_that("calculateOverlapMetric() must return an error when segmentData has metadata status instead of state", {
+    
+    error_message <- paste0("at least one sample doesn't have a metadata column ", 
+                            "called \'state\'")
+    
+    demo <- GRangesList()
+    demo[["sample01"]] <- GRanges(seqnames = "chr1", 
+                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
+                                                    end = c(2004603, 4577608, 31695808)), strand =  "*",
+                                  status = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
+    
+    demo[["sample02"]] <- GRanges(seqnames = "chr1", 
+                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
+                                                    end = c(2004603, 4577608, 31695808)), strand =  "*",
+                                  status= c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
+    
+    expect_error(calculateOverlapMetric(demo), error_message) 
+})
+
+test_that("calculateOverlapMetric() must return an error when segmentData doesn't have metadata state", {
+    
+    error_message <- paste0("at least one sample doesn't have a metadata column ", 
+                            "called \'state\'")
+    
+    demo <- GRangesList()
+    demo[["sample01"]] <- GRanges(seqnames = "chr1", 
+                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
+                                                    end = c(2004603, 4577608, 31695808)), 
+                                  strand =  "*")
+    
+    demo[["sample02"]] <- GRanges(seqnames = "chr1", 
+                                  ranges =  IRanges(start = c(1905048, 4554832, 31686841), 
+                                                    end = c(2004603, 4577608, 31695808)), 
+                                  strand =  "*")
+    
+    expect_error(calculateOverlapMetric(demo), error_message) 
+})
+
+
 ### Tests plotOverlapMetric() results
 
 context("plotOverlapMetric() results")
@@ -178,7 +230,7 @@ test_that("plotOverlapMetric() must return error when type wrong", {
         strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
     
     
-    metric <- calculateOverlapRegionsMetric(segmentData=demo, 
+    metric <- calculateOverlapMetric(segmentData=demo, 
                                                 method="szymkiewicz")
     
     
@@ -212,7 +264,7 @@ test_that("plotOverlapMetric() must return error when colorRange is vector of si
         ranges =  IRanges(start = c(150, 600, 1000), end = c(250, 700, 1500)), 
         strand =  "*", state = c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
     
-    metric <- calculateOverlapRegionsMetric(segmentData = demo, 
+    metric <- calculateOverlapMetric(segmentData = demo, 
                                             method = "szymkiewicz")
     
     error_message <- "\'colorRange\' must be be a vector of 2 valid color names."
@@ -232,7 +284,7 @@ test_that("plotOverlapMetric() must return error when colorRange is vector of on
         ranges=IRanges(start=c(150, 600, 1000), end=c(250, 700, 1500)), 
         strand="*", state=c("AMPLIFICATION", "AMPLIFICATION", "DELETION"))
     
-    metric <- calculateOverlapRegionsMetric(segmentData = demo, 
+    metric <- calculateOverlapMetric(segmentData = demo, 
                                             method = "szymkiewicz")
     
     error_message <- "\'colorRange\' must be a vector of 2 color names."
diff --git a/tests/testthat/test-genericCNVMetric.R b/tests/testthat/test-genericCNVMetric.R
index 5dee05c..ea61d3e 100644
--- a/tests/testthat/test-genericCNVMetric.R
+++ b/tests/testthat/test-genericCNVMetric.R
@@ -29,7 +29,7 @@ test_that("print() for CNVMetric object must return identical object", {
         state = c("AMPLIFICATION", "DELETION"))
 
     ## Calculating Sorensen metric
-    expected <- calculateOverlapRegionsMetric(demo, method="sorensen")
+    expected <- calculateOverlapMetric(demo, method="sorensen")
     
     result <- print(expected)
     
@@ -60,7 +60,7 @@ test_that("is() for CNVMetric object must return identical object", {
                                   state = c("AMPLIFICATION", "DELETION"))
     
     ## Calculating Sorensen metric
-    metric <- calculateOverlapRegionsMetric(demo, method="sorensen")
+    metric <- calculateOverlapMetric(demo, method="sorensen")
     
     result <- is.CNVMetric(metric)