Browse code

minor fix

Simone authored on 09/06/2019 10:58:30
Showing17 changed files

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@@ -23,7 +23,7 @@ License: Artistic-2.0
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 URL: http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/
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 Encoding: UTF-8
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 LazyData: true
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-RoxygenNote: 6.1.0
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+RoxygenNote: 6.1.1
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 Imports:
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     httr,
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     rJava,
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@@ -3,29 +3,17 @@
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 \name{AGGREGATES-Object}
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 \alias{AGGREGATES-Object}
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 \alias{SUM}
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-\alias{AGGREGATES-Object}
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 \alias{COUNT}
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-\alias{AGGREGATES-Object}
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 \alias{COUNTSAMP}
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-\alias{AGGREGATES-Object}
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 \alias{MIN}
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-\alias{AGGREGATES-Object}
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 \alias{MAX}
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-\alias{AGGREGATES-Object}
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 \alias{AVG}
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-\alias{AGGREGATES-Object}
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 \alias{MEDIAN}
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-\alias{AGGREGATES-Object}
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 \alias{STD}
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-\alias{AGGREGATES-Object}
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 \alias{BAG}
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-\alias{AGGREGATES-Object}
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 \alias{BAGD}
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-\alias{AGGREGATES-Object}
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 \alias{Q1}
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-\alias{AGGREGATES-Object}
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 \alias{Q2}
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-\alias{AGGREGATES-Object}
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 \alias{Q3}
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 \title{AGGREGATES object class constructor}
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 \usage{
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@@ -2,7 +2,6 @@
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 % Please edit documentation in R/web-services.R
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 \name{compile_query}
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 \alias{compile_query}
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-\alias{compile_query}
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 \alias{compile_query_fromfile}
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 \title{Compile GMQL query}
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 \usage{
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@@ -3,7 +3,6 @@
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 \name{Cover-Param}
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 \alias{Cover-Param}
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 \alias{ALL}
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-\alias{Cover-Param}
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 \alias{ANY}
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 \title{PARAM object class constructor}
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 \usage{
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@@ -3,7 +3,6 @@
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 \docType{methods}
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 \name{cover}
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 \alias{cover}
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-\alias{cover}
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 \alias{cover,GMQLDataset-method}
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 \title{Method cover}
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 \usage{
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@@ -4,15 +4,10 @@
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 \alias{DISTAL-Object}
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 \alias{DL}
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 \alias{DG}
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-\alias{DISTAL-Object}
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 \alias{DLE}
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-\alias{DISTAL-Object}
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 \alias{DGE}
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-\alias{DISTAL-Object}
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 \alias{MD}
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-\alias{DISTAL-Object}
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 \alias{UP}
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-\alias{DISTAL-Object}
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 \alias{DOWN}
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 \title{DISTAL object class constructor}
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 \usage{
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@@ -4,7 +4,6 @@
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 \name{extend}
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 \alias{extend}
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 \alias{extend,GMQLDataset-method}
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-\alias{extend}
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 \alias{extend-method}
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 \title{Method extend}
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 \usage{
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@@ -46,7 +46,8 @@ from filtering.
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 }
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 \details{
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 This function works only with datatset or GRangesList all whose samples or 
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-Granges have the same region coordinates (chr, ranges, strand)
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+Granges have the same region coordinates (chr, ranges, strand) ordered in 
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+the same way for each sample 
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 In case of GRangesList data input, the function searches for metadata
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 into metadata() function associated to GRangesList.
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@@ -61,10 +62,14 @@ test_path <- system.file("example", "DATASET", package = "RGMQL")
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 filter_and_extract(test_path, region_attributes = c("pvalue", "peak"))
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 ## This statement imports a GMQL dataset as GRangesList and filters it 
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-## including at output only "pvalue" and "peak" region attributes
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+## including at output only "pvalue" and "peak" region attributes, the sort
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+## function makes sure that the region coordinates (chr, ranges, strand) 
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+## of all samples are ordered correctly
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+
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 grl = import_gmql(test_path, TRUE)
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-filter_and_extract(grl, region_attributes = c("pvalue", "peak"))
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+sorted_grl = sort(grl)
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+filter_and_extract(sorted_grl, region_attributes = c("pvalue", "peak"))
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 }
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@@ -4,8 +4,8 @@
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 \alias{init_gmql}
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 \title{Init GMQL server}
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 \usage{
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-init_gmql(output_format = "GTF", remote_processing = FALSE, url = NULL,
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-  username = NULL, password = NULL)
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+init_gmql(output_format = "GTF", remote_processing = FALSE,
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+  url = NULL, username = NULL, password = NULL)
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 }
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 \arguments{
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 \item{output_format}{string that identifies the output format of all sample 
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@@ -22,3 +22,12 @@ After logout the authentication token will be invalidated.
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 The authentication token is removed from R Global environment.
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 If error occurs, a specific error is printed
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 }
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+\examples{
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+
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+## Login to GMQL REST services suite as guest, then logout
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+
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+remote_url = "http://www.gmql.eu/gmql-rest/"
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+login_gmql(remote_url)
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+logout_gmql(remote_url)
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+
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+}
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@@ -4,13 +4,13 @@
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 \name{map}
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 \alias{map}
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 \alias{map,GMQLDataset-method}
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-\alias{map}
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 \alias{map-method}
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 \title{Method map}
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 \usage{
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 map(x, y, ...)
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-\S4method{map}{GMQLDataset}(x, y, ..., joinBy = conds(), count_name = "")
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+\S4method{map}{GMQLDataset}(x, y, ..., joinBy = conds(),
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+  count_name = "")
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 }
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 \arguments{
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 \item{x}{GMQLDataset class object}
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@@ -6,8 +6,9 @@
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 \alias{merge,GMQLDataset,GMQLDataset-method}
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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 = "CAT", joinBy = conds(), reg_attr = c(""))
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+\S4method{merge}{GMQLDataset,GMQLDataset}(x, y,
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+  genometric_predicate = NULL, region_output = "CAT",
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+  joinBy = conds(), reg_attr = c(""))
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 }
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 \arguments{
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 \item{x}{GMQLDataset class object}
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@@ -3,9 +3,7 @@
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 \name{OPERATOR-Object}
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 \alias{OPERATOR-Object}
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 \alias{META}
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-\alias{OPERATOR-Object}
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 \alias{NIL}
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-\alias{OPERATOR-Object}
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 \alias{SQRT}
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 \title{OPERATOR object class constructor}
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 \usage{
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@@ -3,7 +3,6 @@
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 \name{Ordering-Functions}
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 \alias{Ordering-Functions}
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 \alias{DESC}
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-\alias{Ordering-Functions}
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 \alias{ASC}
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 \title{Ordering functions}
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 \usage{
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@@ -2,7 +2,6 @@
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 % Please edit documentation in R/gmql_read.R
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 \name{read_gmql}
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 \alias{read_gmql}
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-\alias{read_gmql}
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 \alias{read_GRangesList}
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 \title{Function read}
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 \usage{
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@@ -2,7 +2,6 @@
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 % Please edit documentation in R/web-services.R
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 \name{run_query}
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 \alias{run_query}
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-\alias{run_query}
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 \alias{run_query_fromfile}
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 \title{Run a GMQL query}
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 \usage{
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@@ -4,7 +4,6 @@
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 \name{take}
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 \alias{take}
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 \alias{take,GMQLDataset-method}
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-\alias{take}
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 \alias{take-method}
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 \title{Method take}
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 \usage{