@@ -35,8 +35,9 @@ execute <- function() {

   WrappeR <- J("it/polimi/genomics/r/Wrapper")

   remote_proc <- WrappeR$is_remote_processing()

   datasets <- .jevalArray(WrappeR$get_dataset_list(), simplify = TRUE)

+  exists_credential <- exists("GMQL_credentials", envir = .GlobalEnv)

-  if(!remote_proc)

+  if(!remote_proc && exists_credential)

     .download_or_upload(datasets)

   response <- WrappeR$execute()

@@ -30,7 +30,11 @@ corresponding prefix.}

 \item{region_attributes}{vector of strings that extracts only region

 attributes  specified; if NULL no regions attribute is taken and the output

 is only GRanges made up by the region coordinate attributes

-(seqnames, start, end, strand)}

+(seqnames, start, end, strand);

+It is also possible to assign the \code{\link{FULL}} with or without 

+its input parameter; in case was without the `except` parameter, 

+all the region attributes are taken, otherwise all the region attributes 

+are taken except the input attribute defined by except.}

 \item{suffix}{name for each metadata column of GRanges. By default it is the

 value of the metadata attribute named "antibody_target". This string is

@@ -75,19 +79,14 @@ grl <- import_gmql(test_path, TRUE)

 sorted_grl <- sort(grl)

 filter_and_extract(sorted_grl, region_attributes = c("pvalue", "peak"))

-## It is also possible to define the region attributes, using the FULL() 

-## function parameter, in order to includes every region 

-## attributes present into the schema file

+## This statement imports a GMQL dataset as GRangesList and filters it

+## including all the region attributes

 sorted_grl_full <- sort(grl)

-filter_and_extract(sorted_grl, region_attributes = FULL())

+filter_and_extract(sorted_grl_full, region_attributes = FULL())

-grl <- import_gmql(test_path, TRUE)

-sorted_grl <- sort(grl)

-filter_and_extract(sorted_grl, region_attributes = FULL())

-

-## Also, we can inlcude a list of region attribute inside the FULL() 

-## function to exlucde that regions

+## This statement imports a GMQL dataset as GRangesList and filters it

+## including all the region attributes except "jaccard" and "score"

 sorted_grl_full_except <- sort(grl)

 filter_and_extract(