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update RD

Simone authored on 27/03/2021 15:11:43
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@@ -1,5 +1,5 @@
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 % Generated by roxygen2: do not edit by hand
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-% Please edit documentation in R/S3Cover-Param.R
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+% Please edit documentation in R/S3filter_extract_param.R
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 \name{filter-extract}
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 \alias{filter-extract}
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 \alias{FULL}
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@@ -19,7 +19,7 @@ to be used in filter and extract function.
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 }
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 \details{
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 It is used to encompasses all the region parameters already present 
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-into the dataset or GrangesList
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+into the dataset or GRangesList
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 \itemize{
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 \item{FULL: It consider all the region paramter}
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@@ -71,8 +71,28 @@ filter_and_extract(test_path, region_attributes = c("pvalue", "peak"))
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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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 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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+## It is also possible to define the region attributes, using the FULL() 
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+## function parameter, in order to includes every region 
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+## attributes present into the schema file
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+
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+sorted_grl_full <- sort(grl)
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+filter_and_extract(sorted_grl, region_attributes = FULL())
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+
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+grl <- import_gmql(test_path, TRUE)
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+sorted_grl <- sort(grl)
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+filter_and_extract(sorted_grl, region_attributes = FULL())
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+
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+## Also, we can inlcude a list of region attribute inside the FULL() 
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+## function to exlucde that regions
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+
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+sorted_grl_full_except <- sort(grl)
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+filter_and_extract(
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+ sorted_grl_full_except, 
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+ region_attributes = FULL("jaccard", "score")
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+)
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+
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 }
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@@ -49,6 +49,21 @@ generated:
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 \item{"provider" = "PoliMi"}
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 \item{"application" = "RGMQL"}
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 }
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+
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+NOTE: 
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+The folder layout must obey the following rules and adopt 
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+the following layout:
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+The dataset folder can have any name, but must contains the 
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+sub-folders named: "files".
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+The sub-folder "files" contains the dataset files and 
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+the schema xml file.
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+The schema files adopt the following the naming conventions:
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+
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+- "schema.xml"
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+- "test.schema"
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+
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+The names must be in LOWERCASE. Any other schema file 
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+will not be conisdered, if both are present, "test.schema" will be used.
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 }
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 \examples{
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@@ -74,4 +89,5 @@ remote_url = "http://www.gmql.eu/gmql-rest/"
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 login_gmql(remote_url)
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 data1 = read_gmql("public.Example_Dataset_1", is_local = FALSE)
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+
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 }
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@@ -41,6 +41,21 @@ a new dataset is created on remote repository
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 \details{
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 If no error occurs, it prints "Upload Complete", otherwise a specific error 
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 is printed
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+
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+NOTE: 
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+The folder layout must obey the following rules and adopt 
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+the following layout:
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+The dataset folder can have any name, but must contains the 
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+sub-folders named: "files".
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+The sub-folder "files" contains the dataset files and 
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+the schema xml file.
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+The schema files adopt the following the naming conventions:
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+
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+- "schema.xml"
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+- "test.schema"
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+
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+The names must be in LOWERCASE. Any other schema file 
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+will not be conisdered, if both are present, "test.schema" will be used.
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 }
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 \examples{
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