@@ -1,16 +1,16 @@

 Package: scTHI

-Title:  Indentification of  significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data. 

-Version:  0.99.6

+Title:  Indentification of  significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data

+Version:  0.99.7

 Authors@R: c(person("Francesca Pia", "Caruso", email = "francescapia.caruso@gmail.com", role = c("aut")),

 	person("Michele", "Ceccarelli", email = "m.ceccarelli@gmail.com", role = c("aut", "cre")))

 Description: scTHI is an R package to identify active pairs of ligand-receptors from single cells in order to study,among others, tumor-host interactions. scTHI contains a set of signatures to classify cells from the tumor microenvironment.

-Depends: scTHI.data, R (>= 4.0)

+Depends:  R (>= 4.0)

 License: GPL-2

 Encoding: UTF-8

 RoxygenNote: 6.1.1.9000

 LazyData: false

 Imports: BiocParallel, Rtsne, grDevices, graphics, stats 

-Suggests: knitr, rmarkdown

+Suggests: scTHI.data, knitr, rmarkdown

 VignetteBuilder: knitr

 biocViews: Software,SingleCell

 BugReports: https://github.com/miccec/scTHI/issues

@@ -27,6 +27,7 @@

 #'  a specific

 #'   phenotype based on the first significant enriched gene set.

 #' @examples

+#' library(scTHI.data)

 #' data(scExample)

 #' Class <- TME_classification(scExample)

 #' @return A list with two items: Class (character) and ClassLegend

@@ -7,6 +7,7 @@

 #' @param Class Object returned by TME_classification function.

 #' @param cexPoint Set the point size.

 #' @examples

+#' library(scTHI.data)

 #' data(scExample)

 #' result <-  scTHI_score(scExample,

 #'            cellCusterA = colnames(scExample)[1:30],

@@ -5,6 +5,7 @@

 #' @param cexPoint Set the point size.

 #' @param legendPos Character string to custom the legend position.

 #' @examples

+#' library(scTHI.data)

 #' data(scExample)

 #' result <-  scTHI_score(scExample,

 #'                        cellCusterA = colnames(scExample)[1:30],

@@ -98,6 +98,7 @@ getcolors <- function(genesToplot, expMat,

 #' @param cexPoint Set the point size.

 #' @param interactionToplot Interaction pair to plot.

 #' @examples

+#' library(scTHI.data)

 #' data(scExample)

 #' result <-  scTHI_score(scExample,

 #'                  cellCusterA = colnames(scExample)[1:30],

@@ -13,6 +13,7 @@

 #'   and partnerB gene, respectively.

 #' @param nRes Number of pairs to plot (all if NULL).

 #' @examples

+#' library(scTHI.data)

 #' data(scExample)

 #' result <-  scTHI_score(scExample,

 #'                        cellCusterA = colnames(scExample)[1:30],

@@ -4,6 +4,7 @@

 #' package.

 #' @param scTHIresult scTHI object.

 #' @examples

+#' library(scTHI.data)

 #' data(scExample)

 #' result <-  scTHI_score(scExample,

 #'                        cellCusterA = colnames(scExample)[1:30],

@@ -129,6 +129,7 @@ getScore <- function(expMat, interaction_table, cellCuster,

 #' @examples

 #'

 #' ####################### example of scTHI_score

+#' library(scTHI.data)

 #' data(scExample)

 #' result <-  scTHI_score(scExample,

 #'       cellCusterA = colnames(scExample)[1:30],

@@ -50,6 +50,7 @@ a collection

 of signatures of different cell types.

 }

 \examples{

+library(scTHI.data)

 data(scExample)

 Class <- TME_classification(scExample)

 }

@@ -21,6 +21,7 @@ Generates a plot on the t-SNE coordinates, labeling cells by TME

 classification.

 }

 \examples{

+library(scTHI.data)

 data(scExample)

 result <-  scTHI_score(scExample,

            cellCusterA = colnames(scExample)[1:30],

@@ -21,6 +21,7 @@ None

 Graphs the output of scTHI_runTsne, labeling cells by clusters.

 }

 \examples{

+library(scTHI.data)

 data(scExample)

 result <-  scTHI_score(scExample,

                        cellCusterA = colnames(scExample)[1:30],

@@ -25,6 +25,7 @@ corresponding

 gene expression value.

 }

 \examples{

+library(scTHI.data)

 data(scExample)

 result <-  scTHI_score(scExample,

                  cellCusterA = colnames(scExample)[1:30],

@@ -30,6 +30,7 @@ None

 Creates barplots of scTHI_score results.

 }

 \examples{

+library(scTHI.data)

 data(scExample)

 result <-  scTHI_score(scExample,

                        cellCusterA = colnames(scExample)[1:30],

@@ -18,6 +18,7 @@ Runs t-SNE dimensionality reduction on selected features based on Rtsne

 package.

 }

 \examples{

+library(scTHI.data)

 data(scExample)

 result <-  scTHI_score(scExample,

                        cellCusterA = colnames(scExample)[1:30],

@@ -61,6 +61,7 @@ cells).

 \examples{

 ####################### example of scTHI_score

+library(scTHI.data)

 data(scExample)

 result <-  scTHI_score(scExample,

       cellCusterA = colnames(scExample)[1:30],