old mode 100644

new mode 100755

@@ -1,9 +1,9 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/gmql_merge.R

-\docType{methods}

 \name{aggregate}

 \alias{aggregate}

 \alias{aggregate,GMQLDataset-method}

+\alias{aggregate-method}

 \title{Method aggregate}

 \usage{

 \S4method{aggregate}{GMQLDataset}(x, groupBy = conds())

@@ -36,7 +36,7 @@ not present in the grouping metadata parameter are disregarded.

 ## 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 file as a GMQL dataset named "exp" 

-## using customParser

+## using CustomParser

 init_gmql()

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

@@ -24,7 +24,7 @@ Wrapper to GMQL MERGE operator

 It builds a dataset consisting of a single sample having as 

 many regions as the number of regions of all the input dataset samples

 and as many metadata as the union of the 'attribute-value' tuples of the 

-input samples. If \emph{groupBy} is specified: the samples are then 

+input samples. If \emph{groupBy} is specified, the samples are then 

 partitioned in groups, each with a distinct value of the grouping metadata 

 attributes. The operation is separately applied to each group, yielding 

 one sample in the result for each group. Samples whose metadata are 

@@ -39,16 +39,15 @@ not present in the grouping metadata parameter are disregarded.

 ## using customParser

 init_gmql()

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

-exp = read_GMQL(test_path)

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

+exp = read_gmql(test_path)

 ## This statement creates a dataset called merged which contains one 

 ## sample for each antibody_target and cell value found within the metadata 

 ## of the exp dataset sample; each created sample contains all regions 

 ## from all 'exp' samples with a specific value for their 

-## antibody_target and cell metadata

-## attributes.

+## antibody_target and cell metadata attributes.

-merged = aggregate(exp, conds(c("antibody_target","cell")))

+merged = aggregate(exp, conds(c("antibody_target", "cell")))

 }

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

 \alias{aggregate,GMQLDataset-method}

 \title{Method aggregate}

 \usage{

-\S4method{aggregate}{GMQLDataset}(x, groupBy = NULL)

+\S4method{aggregate}{GMQLDataset}(x, groupBy = conds())

 }

 \arguments{

 \item{x}{GMQLDataset class object}

@@ -40,7 +40,7 @@ not present in the grouping metadata parameter are disregarded.

 init_gmql()

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

-exp = read_dataset(test_path)

+exp = read_GMQL(test_path)

 ## This statement creates a dataset called merged which contains one 

 ## sample for each antibody_target and cell value found within the metadata 

@@ -49,6 +49,6 @@ exp = read_dataset(test_path)

 ## antibody_target and cell metadata

 ## attributes.

-merged = aggregate(exp, condition_evaluation(c("antibody_target","cell")))

+merged = aggregate(exp, conds(c("antibody_target","cell")))

 }

@@ -11,16 +11,8 @@

 \arguments{

 \item{x}{GMQLDataset class object}

-\item{groupBy}{list of evalation functions to define evaluation on metadata:

-\itemize{

-\item{\code{\link{FN}}(value): Fullname evaluation, two attributes match 

-if they both end with \emph{value} and, if they have further prefixes,

-the two prefix sequences are identical}

-\item{\code{\link{EX}}(value): Exact evaluation, only attributes exactly 

-as \emph{value} match; no further prefixes are allowed. }

-\item{\code{\link{DF}}(value): Default evaluation, the two attributes match 

-if both end with \emph{value}.}

-}}

+\item{groupBy}{\code{\link{condition_evaluation}} function to support 

+methods with groupBy or JoinBy input paramter}

 }

 \value{

 GMQLDataset object. It contains the value to use as input 

@@ -57,6 +49,6 @@ exp = read_dataset(test_path)

 ## antibody_target and cell metadata

 ## attributes.

-merged = aggregate(exp, list(DF("antibody_target","cell")))

+merged = aggregate(exp, condition_evaluation(c("antibody_target","cell")))

 }

new file mode 100644

@@ -0,0 +1,62 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/gmql_merge.R

+\docType{methods}

+\name{aggregate}

+\alias{aggregate}

+\alias{aggregate,GMQLDataset-method}

+\title{Method aggregate}

+\usage{

+\S4method{aggregate}{GMQLDataset}(x, groupBy = NULL)

+}

+\arguments{

+\item{x}{GMQLDataset class object}

+

+\item{groupBy}{list of evalation functions to define evaluation on metadata:

+\itemize{

+\item{\code{\link{FN}}(value): Fullname evaluation, two attributes match 

+if they both end with \emph{value} and, if they have further prefixes,

+the two prefix sequences are identical}

+\item{\code{\link{EX}}(value): Exact evaluation, only attributes exactly 

+as \emph{value} match; no further prefixes are allowed. }

+\item{\code{\link{DF}}(value): Default evaluation, the two attributes match 

+if both end with \emph{value}.}

+}}

+}

+\value{

+GMQLDataset object. It contains the value to use as input 

+for the subsequent GMQLDataset method

+}

+\description{

+Wrapper to GMQL MERGE operator

+

+It builds a dataset consisting of a single sample having as 

+many regions as the number of regions of all the input dataset samples

+and as many metadata as the union of the 'attribute-value' tuples of the 

+input samples. If \emph{groupBy} is specified: the samples are then 

+partitioned in groups, each with a distinct value of the grouping metadata 

+attributes. The operation is separately applied to each group, yielding 

+one sample in the result for each group. Samples whose metadata are 

+not present in the grouping metadata parameter are disregarded.

+}

+\examples{

+

+## This statement initializes and runs the GMQL server for local execution 

+## 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 file as a GMQL dataset named "exp" 

+## using customParser

+

+init_gmql()

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

+exp = read_dataset(test_path)

+

+## This statement creates a dataset called merged which contains one 

+## sample for each antibody_target and cell value found within the metadata 

+## of the exp dataset sample; each created sample contains all regions 

+## from all 'exp' samples with a specific value for their 

+## antibody_target and cell metadata

+## attributes.

+

+merged = aggregate(exp, list(DF("antibody_target","cell")))

+

+}