@@ -4,57 +4,57 @@

 AGGREGATES <- function(value) {

-  op_list <- list(value = value)

-  ## Set the name for the class

-  class(op_list) <- "AGGREGATES"

-  return(op_list)

+    op_list <- list(value = value)

+    ## Set the name for the class

+    class(op_list) <- "AGGREGATES"

+    return(op_list)

 }

 check.META_AGGREGATES <- function(value) {

-  if(is.character(value) && length(value)>1)

-    stop("value: no multiple string")

-  

-  if(!is.character(value))

-    stop("value: is not a string")

+    if(is.character(value) && length(value)>1)

+        stop("value: no multiple string")

+    

+    if(!is.character(value))

+        stop("value: is not a string")

 }

 META_AGGREGATES <- function(value) {

-  op_list <- list(value = value)

-  ## Set the name for the class

-  class(op_list) <- "META_AGGREGATES"

-  return(op_list)

+    op_list <- list(value = value)

+    ## Set the name for the class

+    class(op_list) <- "META_AGGREGATES"

+    return(op_list)

 }

 print.META_AGGREGATES <- function(obj) {

-  res <- as.character(obj)

-  cat(res)

+    res <- as.character(obj)

+    cat(res)

 }

 as.character.META_AGGREGATES <- function(obj) {

-  class <- class(obj)[1]

-  val <- obj$value

-  c(class,val)

+    class <- class(obj)[1]

+    val <- obj$value

+    c(class,val)

 }

 take_value.META_AGGREGATES <- function(obj){

-  class <- class(obj)[1]

-  val <- obj$value

-  text <- switch(

-    class,

-    "SUM" = paste0("sum_",val),

-    "MIN" = paste0("min_",val),

-    "MAX" = paste0("max_",val),

-    "COUNT" = paste0("count"),

-    "BAG" = paste0("bag_",val),

-    "BAGD" = paste0("bagd_",val),

-    "AVG" = paste0("avg_",val),

-    "STD" = paste0("std_"),

-    "MEDIAN" = paste0("median_",val),

-    "Q1" = paste0("q1_",val),

-    "Q2" = paste0("q2_"),

-    "Q3" = paste0("q3_",val)

-  )

-  text

+    class <- class(obj)[1]

+    val <- obj$value

+    text <- switch(

+        class,

+        "SUM" = paste0("sum_",val),

+        "MIN" = paste0("min_",val),

+        "MAX" = paste0("max_",val),

+        "COUNT" = paste0("count"),

+        "BAG" = paste0("bag_",val),

+        "BAGD" = paste0("bagd_",val),

+        "AVG" = paste0("avg_",val),

+        "STD" = paste0("std_"),

+        "MEDIAN" = paste0("median_",val),

+        "Q1" = paste0("q1_",val),

+        "Q2" = paste0("q2_"),

+        "Q3" = paste0("q3_",val)

+    )

+    text

 }

@@ -169,12 +169,12 @@ take_value.META_AGGREGATES <- function(obj){

 #' @export

 #'

 SUM <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("SUM","AGGREGATES","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("SUM","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -183,14 +183,14 @@ SUM <- function(value) {

 #' @export

 #'

 COUNT <- function() {

-  list <- list()

-  ## Set the name for the class

-  class(list) <- c("COUNT","AGGREGATES","META_AGGREGATES")

-  return(list)

+    list <- list()

+    ## Set the name for the class

+    class(list) <- c("COUNT","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

 as.character.COUNT <- function(obj) {

-  class <- class(obj)[1]

-  c(class,"")

+    class <- class(obj)[1]

+    c(class,"")

 }

 check.COUNT <- function(obj){}

@@ -201,14 +201,14 @@ check.COUNT <- function(obj){}

 #' @export

 #'

 COUNTSAMP <- function() {

-  list <- list()

-  ## Set the name for the class

-  class(list) <- c("COUNTSAMP","AGGREGATES","META_AGGREGATES")

-  return(list)

+    list <- list()

+    ## Set the name for the class

+    class(list) <- c("COUNTSAMP","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

 as.character.COUNTSAMP <- function(obj) {

-  class <- class(obj)[1]

-  c(class,"")

+    class <- class(obj)[1]

+    c(class,"")

 }

 check.COUNTSAMP <- function(obj){}

@@ -219,12 +219,12 @@ check.COUNTSAMP <- function(obj){}

 #' @export

 #'

 MIN <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("MIN","AGGREGATES","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("MIN","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -233,12 +233,12 @@ MIN <- function(value) {

 #' @export

 #'

 MAX <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("MAX","AGGREGATES","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("MAX","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -247,12 +247,12 @@ MAX <- function(value) {

 #' @export

 #'

 AVG <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("AVG","AGGREGATES","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("AVG","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -261,12 +261,12 @@ AVG <- function(value) {

 #' @export

 #'

 MEDIAN <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("MEDIAN","AGGREGATES","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("MEDIAN","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

@@ -276,12 +276,12 @@ MEDIAN <- function(value) {

 #' @export

 #'

 STD <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("STD","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("STD","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -290,12 +290,12 @@ STD <- function(value) {

 #' @export

 #'

 BAG <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("BAG","AGGREGATES","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("BAG","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -304,12 +304,12 @@ BAG <- function(value) {

 #' @export

 #'

 BAGD <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("BAGD","AGGREGATES","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("BAGD","AGGREGATES","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -318,12 +318,12 @@ BAGD <- function(value) {

 #' @export

 #'

 Q1 <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("Q1","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("Q1","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -332,11 +332,11 @@ Q1 <- function(value) {

 #' @export

 #'

 Q2 <- function(value) {

-  check.META_AGGREGATES(value)

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("Q2","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("Q2","META_AGGREGATES")

+    return(list)

 }

 #' @name AGGREGATES-Object

@@ -345,10 +345,10 @@ Q2 <- function(value) {

 #' @export

 #'

 Q3 <- function(value) {

-  check.META_AGGREGATES(value)

-  

-  list <- list(value = value)

-  ## Set the name for the class

-  class(list) <- c("Q3","META_AGGREGATES")

-  return(list)

+    check.META_AGGREGATES(value)

+    

+    list <- list(value = value)

+    ## Set the name for the class

+    class(list) <- c("Q3","META_AGGREGATES")

+    return(list)

 }

old mode 100644

new mode 100755

@@ -3,64 +3,61 @@

 ############################

-AGGREGATES <- function(value)

-{

-    op_list <- list(value = value)

-    ## Set the name for the class

-    class(op_list) <- "AGGREGATES"

-    return(op_list)

+AGGREGATES <- function(value) {

+  op_list <- list(value = value)

+  ## Set the name for the class

+  class(op_list) <- "AGGREGATES"

+  return(op_list)

 }

-check.META_AGGREGATES <- function(value)

-{

-    if(is.character(value) && length(value)>1)

-        stop("value: no multiple string")

-    

-    if(!is.character(value))

-        stop("value: is not a string")

+check.META_AGGREGATES <- function(value) {

+  if(is.character(value) && length(value)>1)

+    stop("value: no multiple string")

+  

+  if(!is.character(value))

+    stop("value: is not a string")

 }

-META_AGGREGATES <- function(value)

-{

-    op_list <- list(value = value)

-    ## Set the name for the class

-    class(op_list) <- "META_AGGREGATES"

-    return(op_list)

+META_AGGREGATES <- function(value) {

+  op_list <- list(value = value)

+  ## Set the name for the class

+  class(op_list) <- "META_AGGREGATES"

+  return(op_list)

 }

 print.META_AGGREGATES <- function(obj) {

-    res <- as.character(obj)

-    cat(res)

+  res <- as.character(obj)

+  cat(res)

 }

 as.character.META_AGGREGATES <- function(obj) {

-    class <- class(obj)[1]

-    val <- obj$value

-    c(class,val)

+  class <- class(obj)[1]

+  val <- obj$value

+  c(class,val)

 }

 take_value.META_AGGREGATES <- function(obj){

-    class <- class(obj)[1]

-    val <- obj$value

-    text <- switch(class,

-                "SUM" = paste0("sum_",val),

-                "MIN" = paste0("min_",val),

-                "MAX" = paste0("max_",val),

-                "COUNT" = paste0("count"),

-                "BAG" = paste0("bag_",val),

-                "BAGD" = paste0("bagd_",val),

-                "AVG" = paste0("avg_",val),

-                "STD" = paste0("std_"),

-                "MEDIAN" = paste0("median_",val),

-                "Q1" = paste0("q1_",val),

-                "Q2" = paste0("q2_"),

-                "Q3" = paste0("q3_",val)

-    )

-    text

+  class <- class(obj)[1]

+  val <- obj$value

+  text <- switch(

+    class,

+    "SUM" = paste0("sum_",val),

+    "MIN" = paste0("min_",val),

+    "MAX" = paste0("max_",val),

+    "COUNT" = paste0("count"),

+    "BAG" = paste0("bag_",val),

+    "BAGD" = paste0("bagd_",val),

+    "AVG" = paste0("avg_",val),

+    "STD" = paste0("std_"),

+    "MEDIAN" = paste0("median_",val),

+    "Q1" = paste0("q1_",val),

+    "Q2" = paste0("q2_"),

+    "Q3" = paste0("q3_",val)

+  )

+  text

 }

-

 #' AGGREGATES object class constructor

 #' 

 #' 

@@ -171,14 +168,13 @@ take_value.META_AGGREGATES <- function(obj){

 #' @rdname aggr-class

 #' @export

 #'

-SUM <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("SUM","AGGREGATES","META_AGGREGATES")

-    return(list)

+SUM <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("SUM","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

 #' @name AGGREGATES-Object

@@ -186,16 +182,15 @@ SUM <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-COUNT <- function()

-{

-    list <- list()

-    ## Set the name for the class

-    class(list) <- c("COUNT","AGGREGATES","META_AGGREGATES")

-    return(list)

+COUNT <- function() {

+  list <- list()

+  ## Set the name for the class

+  class(list) <- c("COUNT","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

 as.character.COUNT <- function(obj) {

-    class <- class(obj)[1]

-    c(class,"")

+  class <- class(obj)[1]

+  c(class,"")

 }

 check.COUNT <- function(obj){}

@@ -205,16 +200,15 @@ check.COUNT <- function(obj){}

 #' @rdname aggr-class

 #' @export

 #'

-COUNTSAMP <- function()

-{

-    list <- list()

-    ## Set the name for the class

-    class(list) <- c("COUNTSAMP","AGGREGATES","META_AGGREGATES")

-    return(list)

+COUNTSAMP <- function() {

+  list <- list()

+  ## Set the name for the class

+  class(list) <- c("COUNTSAMP","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

 as.character.COUNTSAMP <- function(obj) {

-    class <- class(obj)[1]

-    c(class,"")

+  class <- class(obj)[1]

+  c(class,"")

 }

 check.COUNTSAMP <- function(obj){}

@@ -224,30 +218,27 @@ check.COUNTSAMP <- function(obj){}

 #' @rdname aggr-class

 #' @export

 #'

-MIN <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("MIN","AGGREGATES","META_AGGREGATES")

-    return(list)

+MIN <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("MIN","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

-

 #' @name AGGREGATES-Object

 #' @aliases MAX

 #' @rdname aggr-class 

 #' @export

 #'

-MAX <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("MAX","AGGREGATES","META_AGGREGATES")

-    return(list)

+MAX <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("MAX","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

 #' @name AGGREGATES-Object

@@ -255,14 +246,13 @@ MAX <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-AVG <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("AVG","AGGREGATES","META_AGGREGATES")

-    return(list)

+AVG <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("AVG","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

 #' @name AGGREGATES-Object

@@ -270,14 +260,13 @@ AVG <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-MEDIAN <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("MEDIAN","AGGREGATES","META_AGGREGATES")

-    return(list)

+MEDIAN <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("MEDIAN","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

@@ -286,14 +275,13 @@ MEDIAN <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-STD <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("STD","META_AGGREGATES")

-    return(list)

+STD <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("STD","META_AGGREGATES")

+  return(list)

 }

 #' @name AGGREGATES-Object

@@ -301,14 +289,13 @@ STD <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-BAG <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("BAG","AGGREGATES","META_AGGREGATES")

-    return(list)

+BAG <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("BAG","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

 #' @name AGGREGATES-Object

@@ -316,14 +303,13 @@ BAG <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-BAGD <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("BAGD","AGGREGATES","META_AGGREGATES")

-    return(list)

+BAGD <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("BAGD","AGGREGATES","META_AGGREGATES")

+  return(list)

 }

 #' @name AGGREGATES-Object

@@ -331,14 +317,13 @@ BAGD <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-Q1 <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("Q1","META_AGGREGATES")

-    return(list)

+Q1 <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("Q1","META_AGGREGATES")

+  return(list)

 }

 #' @name AGGREGATES-Object

@@ -346,13 +331,12 @@ Q1 <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-Q2 <- function(value)

-{

-    check.META_AGGREGATES(value)

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("Q2","META_AGGREGATES")

-    return(list)

+Q2 <- function(value) {

+  check.META_AGGREGATES(value)

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("Q2","META_AGGREGATES")

+  return(list)

 }

 #' @name AGGREGATES-Object

@@ -360,14 +344,11 @@ Q2 <- function(value)

 #' @rdname aggr-class

 #' @export

 #'

-Q3 <- function(value)

-{

-    check.META_AGGREGATES(value)

-    

-    list <- list(value = value)

-    ## Set the name for the class

-    class(list) <- c("Q3","META_AGGREGATES")

-    return(list)

+Q3 <- function(value) {

+  check.META_AGGREGATES(value)

+  

+  list <- list(value = value)

+  ## Set the name for the class

+  class(list) <- c("Q3","META_AGGREGATES")

+  return(list)

 }

-

-

@@ -109,26 +109,26 @@ take_value.META_AGGREGATES <- function(obj){

 #' ## and creation of results on disk. Then, with system.file() it defines 

 #' ## the path to the folder "DATASET" in the subdirectory "example"

 #' ## of the package "RGMQL" and opens such folder as a GMQL dataset 

-#' ## named "exp" using customParser

+#' ## named "exp" using CustomParser

 #' 

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

 #' exp = read_gmql(test_path)

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, and 

-#' ## then calculates new metadata attribute 'sum_score' for each of them: 

+#' ## then calculates new metadata attribute sum_score for each of them: 

 #' ## sum_score is the sum of score values of the sample regions.

 #' 

 #' res = extend(exp, sum_score = SUM("score"))

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, 

-#' ## and then calculates new metadata attribute 'min_pvalue' for each of them: 

+#' ## and then calculates new metadata attribute min_pvalue for each of them: 

 #' ## min_pvalue is the minimum pvalue of the sample regions.

 #' 

 #' res = extend(exp, min_pvalue = MIN("pvalue"))

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, 

-#' ## and then calculates new metadata attribute 'max_score' for each of them: 

+#' ## and then calculates new metadata attribute max_score for each of them: 

 #' ## max_score is the maximum score of the sample regions.

 #' 

 #' res = extend(exp, max_score = MAX("score"))

@@ -148,19 +148,19 @@ take_value.META_AGGREGATES <- function(obj){

 #' out = extend(exp, allScore = BAG("score"))

 #' 

 #' ## This statement counts the regions in each sample and stores their number 

-#' ## as value of the new metadata 'RegionCount' attribute of the sample.

+#' ## as value of the new metadata RegionCount attribute of the sample.

 #' 

 #' out = extend(exp, RegionCount = COUNT())

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, 

-#' ## and then calculates new metadata attribute 'std_score' for each of them: 

+#' ## and then calculates new metadata attribute std_score for each of them: 

 #' ## std_score is the standard deviation of the score values of the sample 

 #' ## regions.

 #' 

 #' res = extend(exp, std_score = STD("score"))

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, 

-#' ## and then calculates new metadata attribute 'm_score' for each of them: 

+#' ## and then calculates new metadata attribute m_score for each of them: 

 #' ## m_score is the median score of the sample regions.

 #' 

 #' res = extend(exp, m_score = MEDIAN("score"))

@@ -73,7 +73,8 @@ take_value.META_AGGREGATES <- function(obj){

 #' \item{COUNT: It prepares input parameter to be passed to the library 

 #' function count, performing all the type conversions needed }

 #' \item{COUNTSAMP: It prepares input parameter to be passed to the library 

-#' function third quartile, performing all the type conversions needed }

+#' function countsamp, performing all the type conversions needed.

+#' It is used only with group_by functions}

 #' \item{MIN: It prepares input parameter to be passed to the library 

 #' function minimum, performing all the type conversions needed  }

 #' \item{MAX: It prepares input parameter to be passed to the library 

@@ -88,7 +89,7 @@ take_value.META_AGGREGATES <- function(obj){

 #' function bag; this function creates comma-separated strings of 

 #' attribute values, performing all the type conversions needed}

 #' \item{BAGD: It prepares input parameter to be passed to the library 

-#' function bag; this function creates comma-separated strings of distinct 

+#' function bagd; this function creates comma-separated strings of distinct 

 #' attribute values, performing all the type conversions needed}

 #' \item{Q1: It prepares input parameter to be passed to the library 

 #' function fist quartile, performing all the type conversions needed}

@@ -112,22 +113,22 @@ take_value.META_AGGREGATES <- function(obj){

 #' 

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

-#' exp = read_GMQL(test_path)

+#' exp = read_gmql(test_path)

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, and 

-#' ## then calculates new metadata attribute for each of them: 

-#' ## sum_score is the sum of score of the sample regions.

+#' ## then calculates new metadata attribute 'sum_score' for each of them: 

+#' ## sum_score is the sum of score values of the sample regions.

 #' 

 #' res = extend(exp, sum_score = SUM("score"))

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, 

-#' ## and then calculates new metadata attribute for each of them: 

+#' ## and then calculates new metadata attribute 'min_pvalue' for each of them: 

 #' ## min_pvalue is the minimum pvalue of the sample regions.

 #' 

 #' res = extend(exp, min_pvalue = MIN("pvalue"))

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, 

-#' ## and then calculates new metadata attribute for each of them: 

+#' ## and then calculates new metadata attribute 'max_score' for each of them: 

 #' ## max_score is the maximum score of the sample regions.

 #' 

 #' res = extend(exp, max_score = MAX("score"))

@@ -135,30 +136,31 @@ take_value.META_AGGREGATES <- function(obj){

 #' ## The following cover operation produces output regions where at least 2 

 #' ## and at most 3 regions of exp dataset overlap, having as resulting region 

 #' ## attribute the average signal of the overlapping regions; 

-#' ## the result has one sample for each input cell.

+#' ## the result has one sample for each input cell value.

 #' 

 #' res = cover(exp, 2, 3, groupBy = conds("cell"), avg_signal = AVG("signal"))

 #' 

-#' ## This statement copies all samples of DATA dataset into OUT dataset, 

-#' ## and then for each of them it adds another metadata attribute, allScores, 

+#' ## This statement copies all samples of 'exp' dataset into 'out' dataset, 

+#' ## and then for each of them it adds another metadata attribute, allScore, 

 #' ## which is the aggregation comma-separated list of all the values 

 #' ## that the region attribute score takes in the sample.

 #' 

 #' out = extend(exp, allScore = BAG("score"))

 #' 

 #' ## This statement counts the regions in each sample and stores their number 

-#' ## as value of the new metadata RegionCount attribute of the sample.

+#' ## as value of the new metadata 'RegionCount' attribute of the sample.

 #' 

 #' out = extend(exp, RegionCount = COUNT())

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, 

-#' ## and then calculates new metadata attribute for each of them: 

-#' ## std_score is the standard deviation score of the sample regions.

+#' ## and then calculates new metadata attribute 'std_score' for each of them: 

+#' ## std_score is the standard deviation of the score values of the sample 

+#' ## regions.

 #' 

 #' res = extend(exp, std_score = STD("score"))

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, 

-#' ## and then calculates new metadata attribute for each of them: 

+#' ## and then calculates new metadata attribute 'm_score' for each of them: 

 #' ## m_score is the median score of the sample regions.

 #' 

 #' res = extend(exp, m_score = MEDIAN("score"))

@@ -112,7 +112,7 @@ take_value.META_AGGREGATES <- function(obj){

 #' 

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

-#' exp = read_dataset(test_path)

+#' exp = read_GMQL(test_path)

 #' 

 #' ## This statement copies all samples of exp dataset into res dataset, and 

 #' ## then calculates new metadata attribute for each of them: 

@@ -137,8 +137,7 @@ take_value.META_AGGREGATES <- function(obj){

 #' ## attribute the average signal of the overlapping regions;