diff --git a/NAMESPACE b/NAMESPACE
index 0174144..de3f16a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,4 +9,4 @@ export(multiSampleComparisonClonalCN)
 export(pipelineCNA)
 export(plotAllSubclonalCN)
 export(top30classification)
-useDynLib(SCEVAN, .registration=TRUE)
\ No newline at end of file
+useDynLib(SCEVAN, .registration=TRUE)
diff --git a/R/pipelineCNA.R b/R/pipelineCNA.R
index 7b06ef3..cdd2838 100644
--- a/R/pipelineCNA.R
+++ b/R/pipelineCNA.R
@@ -12,18 +12,16 @@ NULL
 #> NULL
 
 
-
-
 #' pipelineCNA Executes the entire SCEVAN pipeline that classifies tumour and normal cells from the raw count matrix, infer the clonal profile of cancer cells and looks for possible sub-clones in the tumour cell matrix automatically analysing the specific and shared alterations of each subclone and a differential analysis of pathways and genes expressed in each subclone.
 #'
-#' @param count_mtx raw count matrix
-#' @param sample sample name (optional)
-#' @param par_cores number of cores (default 20)
-#' @param norm_cell vector of normal cells if already known (optional)
-#' @param SUBCLONES find subclones (default TRUE)
-#' @param beta_vega specifies beta parameter for segmentation, higher beta for more coarse-grained segmentation. (default 0.5) 
-#' @param ClonalCN clonal profile inference from tumour cells (optional)
-#' @param plotTree find subclones (optional)
+#' @param count_mtx Raw count matrix with genes on rows (both Gene Symbol or Ensembl ID are allowed) and cells on columns.
+#' @param sample Sample name to save results (optional)
+#' @param par_cores Number of cores to run the pipeline (optional - default 20)
+#' @param norm_cell Vector of normal cells if the classification is already known and you are only interested in the clonal structure (optional)
+#' @param SUBCLONES Boolean value TRUE if you are interested in analysing the clonal structure and FALSE if you are only interested in the classification of malignant and non-malignant cells (optional - default TRUE)
+#' @param beta_vega Specifies beta parameter for segmentation, higher beta for more coarse-grained segmentation. (optional - default 0.5)
+#' @param ClonalCN Get clonal CN profile inference from all tumour cells (optional)
+#' @param plotTree Plot Phylogenetic tree (optional - default FALSE)
 #' @param AdditionalGeneSets list of additional signatures of normal cell types (optional)
 #' @param SCEVANsignatures FALSE if you only want to use only the signatures specified in AdditionalGeneSets (default TRUE)
 #' @param organism Organism to be analysed (optional - "mouse" or "human" - default "human")
diff --git a/README.md b/README.md
index 10e7ead..d6de3d4 100644
--- a/README.md
+++ b/README.md
@@ -27,14 +27,14 @@ A single call (pipelineCNA) allows the execution of the entire analysis of class
 - ***count_mtx*** : Count matrix with genes on rows (both Gene Symbol or Ensembl ID are allowed) and cells on columns.
 - ***sample*** : Sample name to save results (optional)
 - ***par_cores*** : Number of cores to run the pipeline  (optional - default 20)
-- ***norm_cells*** : vectors of normal cells if the classification is already known and you are only interested in the clonal structure (optional)
-- ***SUBCLONES*** : Boolean value TRUE if you are interested in analysing the clonal structure and FALSE if you are only interested in the classification of malignant and non-malignant cells (optional - default 20)
+- ***norm_cells*** : Vector of normal cells if the classification is already known and you are only interested in the clonal structure (optional)
+- ***SUBCLONES*** : Boolean value TRUE if you are interested in analysing the clonal structure and FALSE if you are only interested in the classification of malignant and non-malignant cells (optional - default TRUE)
 - ***beta_vega*** : Specifies beta parameter for segmentation, higher beta for more coarse-grained segmentation. (optional - default 0.5)
 - ***ClonalCN*** :  Get clonal CN profile inference from all tumour cells (optional)
 - ***plotTree*** : Plot Phylogenetic tree (optional - default FALSE) 
 - ***AdditionalGeneSets*** : list of additional signatures of normal cell types (optional)
 - ***SCEVANsignatures*** : FALSE if you only want to use only the signatures specified in AdditionalGeneSets(optional - default TRUE) 
-- ***organism*** : Organism to be analysed (optional - default human)
+- ***organism*** : Organism to be analysed (optional - "mouse" or "human" - default "human")
 
 ```
 results <- pipelineCNA(count_mtx)
@@ -45,7 +45,7 @@ A single call (multiSampleComparisonClonalCN) allows the comparison of clonal pr
 
 - ***listCountMtx*** : Named list of raw count matrix of samples to be analysed
 - ***analysisName*** : Name of the analysis (optional)
-- ***organism*** : Organism to be analysed (default human)
+- ***organism*** : Organism to be analysed (optional - "mouse" or "human" - default "human")
 - ***par_cores*** : Number of cores (default 20)
 
 ```
diff --git a/man/pipelineCNA.Rd b/man/pipelineCNA.Rd
index 14c4463..b54b41b 100644
--- a/man/pipelineCNA.Rd
+++ b/man/pipelineCNA.Rd
@@ -19,21 +19,21 @@ pipelineCNA(
 )
 }
 \arguments{
-\item{count_mtx}{raw count matrix}
+\item{count_mtx}{Raw count matrix with genes on rows (both Gene Symbol or Ensembl ID are allowed) and cells on columns.}
 
-\item{sample}{sample name (optional)}
+\item{sample}{Sample name to save results (optional)}
 
-\item{par_cores}{number of cores (default 20)}
+\item{par_cores}{Number of cores to run the pipeline (optional - default 20)}
 
-\item{norm_cell}{vector of normal cells if already known (optional)}
+\item{norm_cell}{Vector of normal cells if the classification is already known and you are only interested in the clonal structure (optional)}
 
-\item{SUBCLONES}{find subclones (default TRUE)}
+\item{SUBCLONES}{Boolean value TRUE if you are interested in analysing the clonal structure and FALSE if you are only interested in the classification of malignant and non-malignant cells (optional - default TRUE)}
 
-\item{beta_vega}{specifies beta parameter for segmentation, higher beta for more coarse-grained segmentation. (default 0.5)}
+\item{beta_vega}{Specifies beta parameter for segmentation, higher beta for more coarse-grained segmentation. (optional - default 0.5)}
 
-\item{ClonalCN}{clonal profile inference from tumour cells (optional)}
+\item{ClonalCN}{Get clonal CN profile inference from all tumour cells (optional)}
 
-\item{plotTree}{find subclones (optional)}
+\item{plotTree}{Plot Phylogenetic tree (optional - default FALSE)}
 
 \item{AdditionalGeneSets}{list of additional signatures of normal cell types (optional)}