| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: RGMQL |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: GenoMetric Query Language for R/Bioconductor |
| 4 |
-Version: 0.99.40 |
|
| 4 |
+Version: 0.99.41 |
|
| 5 | 5 |
Author: Simone Pallotta, Marco Masseroli |
| 6 | 6 |
Maintainer: Simone Pallotta <simonepallotta@hotmail.com> |
| 7 | 7 |
Description: This package brings the GenoMetric Query Language (GMQL) |
| ... | ... |
@@ -23,12 +23,12 @@ group_by.GMQLDateset <- function(.data, groupBy_meta = conds(), |
| 23 | 23 |
#' All the element in the form \emph{key} = \emph{aggregate}.
|
| 24 | 24 |
#' The \emph{aggregate} is an object of class AGGREGATES
|
| 25 | 25 |
#' The aggregate functions available are: \code{\link{SUM}},
|
| 26 |
-#' \code{\link{COUNT}}, \code{\link{MIN}}, \code{\link{MAX}},
|
|
| 26 |
+#' \code{\link{COUNTSAMP}}, \code{\link{MIN}}, \code{\link{MAX}},
|
|
| 27 | 27 |
#' \code{\link{AVG}}, \code{\link{MEDIAN}}, \code{\link{STD}},
|
| 28 | 28 |
#' \code{\link{BAG}}, \code{\link{BAGD}}, \code{\link{Q1}},
|
| 29 | 29 |
#' \code{\link{Q2}}, \code{\link{Q3}}.
|
| 30 |
-#' Every aggregate accepts a string value, execet for COUNT, which does not |
|
| 31 |
-#' have any value. |
|
| 30 |
+#' Every aggregate accepts a string value, execet for COUNTSAMP, which does |
|
| 31 |
+#' not have any value. |
|
| 32 | 32 |
#' Argument of 'aggregate function' must exist in schema, i.e. among region |
| 33 | 33 |
#' attributes. Two style are allowed: |
| 34 | 34 |
#' \itemize{
|
| ... | ... |
@@ -41,12 +41,12 @@ group_by.GMQLDateset <- function(.data, groupBy_meta = conds(), |
| 41 | 41 |
#' All the element in the form \emph{key} = \emph{aggregate}.
|
| 42 | 42 |
#' The \emph{aggregate} is an object of class AGGREGATES
|
| 43 | 43 |
#' The aggregate functions available are: \code{\link{SUM}},
|
| 44 |
-#' \code{\link{COUNT}}, \code{\link{MIN}}, \code{\link{MAX}},
|
|
| 44 |
+#' \code{\link{COUNTSAMP}}, \code{\link{MIN}}, \code{\link{MAX}},
|
|
| 45 | 45 |
#' \code{\link{AVG}}, \code{\link{MEDIAN}}, \code{\link{STD}},
|
| 46 | 46 |
#' \code{\link{BAG}}, \code{\link{BAGD}}, \code{\link{Q1}},
|
| 47 | 47 |
#' \code{\link{Q2}}, \code{\link{Q3}}.
|
| 48 |
-#' Every aggregate accepts a string value, execet for COUNT, which does not |
|
| 49 |
-#' have any value. |
|
| 48 |
+#' Every aggregate accepts a string value, execet for COUNTSAMP, which does |
|
| 49 |
+#' not have any value. |
|
| 50 | 50 |
#' Argument of 'aggregate function' must exist in schema, i.e. among region |
| 51 | 51 |
#' attributes. Two style are allowed: |
| 52 | 52 |
#' \itemize{
|
| ... | ... |
@@ -115,7 +115,7 @@ are disregarded. |
| 115 | 115 |
init_gmql() |
| 116 | 116 |
test_path <- system.file("example","DATASET",package = "RGMQL")
|
| 117 | 117 |
exp = read_GMQL(test_path) |
| 118 |
- |
|
| 118 |
+ |
|
| 119 | 119 |
## the following statement produces an output dataset with a single output |
| 120 | 120 |
## sample. The COVER operation considers all areas defined by a minimum |
| 121 | 121 |
## of two overlapping regions in the input samples, up to any amount of |
| ... | ... |
@@ -23,12 +23,12 @@ region attribute. |
| 23 | 23 |
All the element in the form \emph{key} = \emph{aggregate}.
|
| 24 | 24 |
The \emph{aggregate} is an object of class AGGREGATES
|
| 25 | 25 |
The aggregate functions available are: \code{\link{SUM}},
|
| 26 |
-\code{\link{COUNT}}, \code{\link{MIN}}, \code{\link{MAX}},
|
|
| 26 |
+\code{\link{COUNTSAMP}}, \code{\link{MIN}}, \code{\link{MAX}},
|
|
| 27 | 27 |
\code{\link{AVG}}, \code{\link{MEDIAN}}, \code{\link{STD}},
|
| 28 | 28 |
\code{\link{BAG}}, \code{\link{BAGD}}, \code{\link{Q1}},
|
| 29 | 29 |
\code{\link{Q2}}, \code{\link{Q3}}.
|
| 30 |
-Every aggregate accepts a string value, execet for COUNT, which does not |
|
| 31 |
-have any value. |
|
| 30 |
+Every aggregate accepts a string value, execet for COUNTSAMP, which does |
|
| 31 |
+not have any value. |
|
| 32 | 32 |
Argument of 'aggregate function' must exist in schema, i.e. among region |
| 33 | 33 |
attributes. Two style are allowed: |
| 34 | 34 |
\itemize{
|
| ... | ... |
@@ -42,12 +42,12 @@ metadata attribute. |
| 42 | 42 |
All the element in the form \emph{key} = \emph{aggregate}.
|
| 43 | 43 |
The \emph{aggregate} is an object of class AGGREGATES
|
| 44 | 44 |
The aggregate functions available are: \code{\link{SUM}},
|
| 45 |
-\code{\link{COUNT}}, \code{\link{MIN}}, \code{\link{MAX}},
|
|
| 45 |
+\code{\link{COUNTSAMP}}, \code{\link{MIN}}, \code{\link{MAX}},
|
|
| 46 | 46 |
\code{\link{AVG}}, \code{\link{MEDIAN}}, \code{\link{STD}},
|
| 47 | 47 |
\code{\link{BAG}}, \code{\link{BAGD}}, \code{\link{Q1}},
|
| 48 | 48 |
\code{\link{Q2}}, \code{\link{Q3}}.
|
| 49 |
-Every aggregate accepts a string value, execet for COUNT, which does not |
|
| 50 |
-have any value. |
|
| 49 |
+Every aggregate accepts a string value, execet for COUNTSAMP, which does |
|
| 50 |
+not have any value. |
|
| 51 | 51 |
Argument of 'aggregate function' must exist in schema, i.e. among region |
| 52 | 52 |
attributes. Two style are allowed: |
| 53 | 53 |
\itemize{
|
| ... | ... |
@@ -4,12 +4,12 @@ |
| 4 | 4 |
\alias{semijoin}
|
| 5 | 5 |
\title{Semijoin condtion}
|
| 6 | 6 |
\usage{
|
| 7 |
-semijoin(.data, not_in = FALSE, groupBy) |
|
| 7 |
+semijoin(.data, is_in = TRUE, groupBy) |
|
| 8 | 8 |
} |
| 9 | 9 |
\arguments{
|
| 10 | 10 |
\item{.data}{GMQLDataset class object}
|
| 11 | 11 |
|
| 12 |
-\item{not_in}{logical value: TRUE => for a given sample of input dataset
|
|
| 12 |
+\item{is_in}{logical value: TRUE => for a given sample of input dataset
|
|
| 13 | 13 |
".data" in \code{\link{filter}} method if and only if there exists at
|
| 14 | 14 |
least one sample in dataset 'data' with metadata attributes defined |
| 15 | 15 |
in groupBy and these attributes of 'data' have at least one value in |
