Simone authored on 28/12/2017 14:43:57
Showing13 changed files

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@@ -28,7 +28,7 @@ export(SUM)
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 export(UP)
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 export(compile_query)
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 export(compile_query_fromfile)
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-export(condition_evaluation)
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+export(conds)
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 export(delete_dataset)
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 export(download_as_GRangesList)
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 export(download_dataset)
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@@ -34,7 +34,7 @@
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 #' @aliases condition_evaluation
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 #' @rdname condition_eval_func
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 #' @export
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-condition_evaluation <- function(default = c(""), full = c(""), exact = c(""))
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+conds <- function(default = c(""), full = c(""), exact = c(""))
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 {
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     df <- .condition("DEF",default)
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     fn <- .condition("FULL",full)
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@@ -43,6 +43,20 @@
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 #' having left (right) coordinates equal to the minimum (maximum) of the 
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 #' corresponding coordinate values in the 'x' and 'y' regions satisfying 
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 #' the genometric predicate)}
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+#' \item{LEFT_DISTINCT: It outputs the duplicate elimination of "x" output 
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+#' regions with the same values, regardless the "y" paired region and its 
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+#' values. In this case, the output regions attributes and their values are 
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+#' all those of "x", and the output metadata are equal to the "x" metadata, 
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+#' without additional prefixes}
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+#' \item{RIGHT_DISTINCT: It outputs the duplicate elimination of "y" output 
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+#' regions with the same values, regardless the "x" paired region and its 
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+#' values. In this case, the output regions attributes and their values are 
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+#' all those of "y", and the output metadata are equal to the "y" metadata, 
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+#' without additional prefixes}
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+#' \item{BOTH: It outputs the same regions as LEFT, but it adds in the output 
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+#' region attributes the coordinates of the "y" dataset region that, 
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+#' together with the output "x" dataset region, satisfies the equi predicate 
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+#' and the genometric predicate}
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 #' }
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 #'
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 #' @return GMQLDataset object. It contains the value to use as input 
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@@ -85,13 +99,13 @@ setMethod("merge", c("GMQLDataset","GMQLDataset"),
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                 {
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                     ptr_data_x <- value(x)
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                     ptr_data_y <- value(y)
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-                    gmql_join(ptr_data_x, ptr_data_y, genometric_predicate, 
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-                                joinBy, region_output, reg_attr)
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+                    gmql_join(ptr_data_x, ptr_data_y, 
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+                        genometric_predicate, joinBy, region_output, reg_attr)
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                 })
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 gmql_join <- function(left_data, right_data, genometric_predicate, joinBy, 
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-                            region_output, reg_attributes)
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+                        region_output, reg_attributes)
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 {
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     if(!is.null(genometric_predicate))
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     {
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@@ -49,6 +49,8 @@
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 #' \item{ \code{\link{DF}}(value): Default evaluation, the two attributes match 
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 #' if both end with \emph{value}.}
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 #' }
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+#' @param count_name string defining the metadata count name; if it is 
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+#' not specifying the name is "count_left_right" 
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 #' 
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 #' @return GMQLDataset object. It contains the value to use as input 
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 #' for the subsequent GMQLDataset method
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@@ -84,16 +86,16 @@
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 #' @aliases map-method
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 #' @export
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 setMethod("map", "GMQLDataset",
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-            function(x, y, ..., joinBy = NULL)
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+            function(x, y, ..., joinBy = NULL, count_name = NULL)
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             {
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                 left_data <- value(x)
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                 right_data <- value(y)
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                 aggregates = list(...)
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-                gmql_map(left_data, right_data, aggregates, joinBy)
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+                gmql_map(left_data, right_data,aggregates, joinBy, count_name)
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             })
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-gmql_map <- function(left_data, right_data, aggregates, joinBy)
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+gmql_map <- function(left_data, right_data, aggregates, joinBy, count_name)
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 {
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     if(!is.null(aggregates) && length(aggregates))
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     {
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@@ -114,8 +116,17 @@ gmql_map <- function(left_data, right_data, aggregates, joinBy)
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     else
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         join_matrix <- .jnull("java/lang/String")
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+    if(!is.null(count_name))
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+    {
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+        if(!is.character(count_name))
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+            stop("count_name: must be string")
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+    }
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+    else
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+        count_name <- .jnull("java/lang/String")
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+    
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     WrappeR <- J("it/polimi/genomics/r/Wrapper")
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-    response<-WrappeR$map(join_matrix, metadata_matrix, left_data, right_data)
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+    response<-WrappeR$map(join_matrix, metadata_matrix, count_name, left_data, 
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+                            right_data)
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     error <- strtoi(response[1])
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     val <- response[2]
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     if(error!=0)
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@@ -32,8 +32,8 @@ arrange.GMQLDataset <- function(.data, metadata_ordering = NULL,
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 #' first k samples; it can assume the values:
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 #' \itemize{
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 #' \item{mtop: it fetches the first k samples}
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-#' \item{mtopg: it fetches the percentage of samples.}
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-#' \item{mtopp: it fetches the first k samples in each group.}
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+#' \item{mtopp: it fetches the first k percentage of samples.}
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+#' \item{mtopg: it fetches the first k samples in each group.}
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 #' 
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 #' }
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 #' if NULL, \emph{num_fetch} is not considered 
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@@ -49,8 +49,8 @@ arrange.GMQLDataset <- function(.data, metadata_ordering = NULL,
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 #' first k regions; it can assume the values:
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 #' \itemize{
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 #' \item{rtop: it fetches the first k regions.}
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-#' \item{rtopg: it fetches the first k percentage of regions.}
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-#' \item{rtopp: it fetches the first k regions in each group.}
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+#' \item{rtopp: it fetches the first k percentage of regions.}
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+#' \item{rtopg: it fetches the first k regions in each group.}
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 #' }
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 #' if NULL, \emph{reg_num_fetch} is not considered 
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 #' 
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Binary files a/inst/java/GMQL.jar and b/inst/java/GMQL.jar differ
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@@ -7,8 +7,8 @@
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 \title{Method arrange}
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 \usage{
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 \S4method{arrange}{GMQLDataset}(.data, metadata_ordering = NULL,
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-  regions_ordering = NULL, fetch_opt = NULL, num_fetch = 0,
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-  reg_fetch_opt = NULL, reg_num_fetch = 0)
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+  regions_ordering = NULL, fetch_opt = NULL, num_fetch = 0L,
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+  reg_fetch_opt = NULL, reg_num_fetch = 0L)
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 }
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 \arguments{
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 \item{.data}{GMQLDataset class object}
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@@ -2,25 +2,26 @@
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 % Please edit documentation in R/evaluation-functions.R
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 \name{Evaluation-Function}
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 \alias{Evaluation-Function}
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+\alias{conds}
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 \alias{condition_evaluation}
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 \title{Condition evaluation functions}
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 \usage{
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-condition_evaluation(default = c(""), full = c(""), exact = c(""))
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+conds(default = c(""), full = c(""), exact = c(""))
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 }
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 \arguments{
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-\item{default}{series of string identifying a name of metadata attribute 
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-to be evaluated.
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-It defines a DEFAULT evaluation of the input values.
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+\item{default}{concatenation of string identifying a name of metadata 
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+attribute to be evaluated. 
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+It defines a DEFAULT evaluation of the input values. 
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 DEFAULT evaluation: the two attributes match if both end with value.}
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-\item{full}{series of string identifying a name of metadata attribute 
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-to be evaluated.
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+\item{full}{concatenation of string identifying a name of metadata 
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+attribute to be evaluated.
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 It defines a FULL (FULLNAME) evaluation of the input values.
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 FULL evaluation: two attributes match if they both end with value and,
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 if they have further prefixes, the two prefix sequences are identical.}
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-\item{exact}{series of string identifying a name of metadata attribute 
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-to be evaluated.
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+\item{exact}{concatenation of string identifying a name of metadata 
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+attribute to be evaluated.
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 It defines a EXACT evaluation of the input values.
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 EXACT evaluation: only attributes exactly as value match; 
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 no further prefixes are allowed.}
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@@ -7,13 +7,13 @@
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 \alias{cover,GMQLDataset-method}
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 \title{Method cover}
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 \usage{
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-cover(data, ...)
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+cover(.data, ...)
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-\S4method{cover}{GMQLDataset}(data, min_acc, max_acc, groupBy = NULL,
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+\S4method{cover}{GMQLDataset}(.data, min_acc, max_acc, groupBy = NULL,
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   variation = "cover", ...)
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 }
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 \arguments{
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-\item{data}{GMQLDataset class object}
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+\item{.data}{GMQLDataset class object}
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 \item{...}{a series of expressions separated by comma in the form 
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 \emph{key} = \emph{aggregate}. The \emph{aggregate} is an object of 
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@@ -10,7 +10,7 @@
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 \usage{
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 map(x, y, ...)
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-\S4method{map}{GMQLDataset}(x, y, ..., joinBy = NULL)
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+\S4method{map}{GMQLDataset}(x, y, ..., joinBy = NULL, count_name = NULL)
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 }
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 \arguments{
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 \item{x}{GMQLDataset class object}
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@@ -44,6 +44,9 @@ as \emph{value} match; no further prefixes are allowed.}
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 \item{ \code{\link{DF}}(value): Default evaluation, the two attributes match 
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 if both end with \emph{value}.}
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 }}
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+
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+\item{count_name}{string defining the metadata count name; if it is 
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+not specifying the name is "count_left_right"}
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 }
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 \value{
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 GMQLDataset object. It contains the value to use as input 
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@@ -7,7 +7,7 @@
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 \title{Method merge}
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 \usage{
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 \S4method{merge}{GMQLDataset,GMQLDataset}(x, y, genometric_predicate = NULL,
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-  region_output = "contig", joinBy = NULL)
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+  region_output = "CAT", joinBy = NULL, reg_attr = NULL)
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 }
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 \arguments{
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 \item{x}{GMQLDataset class object}
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@@ -35,10 +35,26 @@ that satisfy the genometric predicate, (i.e. the output regionis defined as
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 having left (right) coordinates equal to the minimum (maximum) of the 
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 corresponding coordinate values in the 'x' and 'y' regions satisfying 
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 the genometric predicate)}
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+\item{LEFT_DISTINCT: It outputs the duplicate elimination of "x" output 
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+regions with the same values, regardless the "y" paired region and its 
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+values. In this case, the output regions attributes and their values are 
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+all those of "x", and the output metadata are equal to the "x" metadata, 
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+without additional prefixes}
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+\item{RIGHT_DISTINCT: It outputs the duplicate elimination of "y" output 
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+regions with the same values, regardless the "x" paired region and its 
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+values. In this case, the output regions attributes and their values are 
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+all those of "y", and the output metadata are equal to the "y" metadata, 
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+without additional prefixes}
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+\item{BOTH: outputs the same regions as LEFT, but it adds in the output 
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+region attributes the coordinates of the "y" dataset region that, 
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+together with the output "x" dataset region, satisfies the equi predicate 
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+and the genometric predicate}
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 }}
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 \item{joinBy}{\code{\link{condition_evaluation}} function to support 
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 methods with groupBy or JoinBy input paramter}
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+
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+\item{reg_attr}{vector of string made up by schema field attribute}
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 }
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 \value{
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 GMQLDataset object. It contains the value to use as input 
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@@ -4,10 +4,10 @@
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 \alias{semijoin}
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 \title{Semijoin condtion}
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 \usage{
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-semijoin(data, not_in = FALSE, groupBy = NULL)
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+semijoin(.data, not_in = FALSE, groupBy = NULL)
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 }
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 \arguments{
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-\item{data}{GMQLDataset class object}
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+\item{.data}{GMQLDataset class object}
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 \item{not_in}{logical value: TRUE => for a given sample of input dataset
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 ".data" in \code{\link{filter}} method if and only if there exists at 
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@@ -8,12 +8,12 @@
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 \alias{take-method}
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 \title{Method take}
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 \usage{
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-take(data, ...)
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+take(.data, ...)
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-\S4method{take}{GMQLDataset}(data, rows = 0L)
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+\S4method{take}{GMQLDataset}(.data, rows = 0L)
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 }
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 \arguments{
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-\item{data}{returned object from any GMQL function}
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+\item{.data}{returned object from any GMQL function}
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 \item{...}{Additional arguments for use in other specific methods of the 
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 generic take function}