@@ -61,6 +61,7 @@ Collate:

     'S3Aggregates.R'

     'S3Cover-Param.R'

     'S3Distal.R'

+    'S3filter_extract_param.R'

     'S3Operator.R'

     'Utils.R'

     'evaluation-functions.R'

@@ -89,30 +89,3 @@ ANY <- function() {

   return(list)

 }

-

-#' PARAM object class constructor

-#'

-#' This class constructor is used to create instances of PARAM object

-#' to be used in filter and extract function.

-#' 

-#' It is used to encompasses all the region parameters already present 

-#' into the dataset or GrangesList

-#' 

-#' \itemize{

-#' \item{FULL: It consider all the region paramter}

-#' }

-#' @param except The list of attribute to not consider

-#' 

-#' @return Param object

-#'

-#' @name filter-extract

-#' @aliases FULL

-#' @rdname filter-extract-param-class

-#' @export

-#'

-FULL <- function(except = NULL) {

-  value <- list(values = c(except))

-  ## Set the name for the class

-  class(value) <- c("FULL", "PARAMETER")

-  return(value)

-}

new file mode 100644

@@ -0,0 +1,46 @@

+##########################################

+#       PARAMETER_FILTER_EXTRACT        #

+#########################################

+

+PARAMETER_FILTER_EXTRACT <- function() {

+  op_list <- list()

+  ## Set the name for the class

+  class(op_list) <- "PARAMETER_FILTER_EXTRACT"

+  return(op_list)

+}

+

+as.character.PARAMETER_FILTER_EXTRACT <- function(obj) {

+  class <- class(obj)[1]

+}

+

+print.PARAMETER_FILTER_EXTRACT <- function(obj){

+  print(as.character.PARAMETER_FILTER_EXTRACT(obj))

+}

+

+

+#' PARAM object class constructor

+#'

+#' This class constructor is used to create instances of PARAM object

+#' to be used in filter and extract function.

+#' 

+#' It is used to encompasses all the region parameters already present 

+#' into the dataset or GRangesList

+#' 

+#' \itemize{

+#' \item{FULL: It consider all the region paramter}

+#' }

+#' @param except The list of attribute to not consider

+#' 

+#' @return Param object

+#'

+#' @name filter-extract

+#' @aliases FULL

+#' @rdname filter-extract-param-class

+#' @export

+#'

+FULL <- function(except = NULL) {

+  value <- list(values = c(except))

+  ## Set the name for the class

+  class(value) <- c("FULL", "PARAMETER_FILTER_EXTRACT")

+  return(value)

+}

\ No newline at end of file

@@ -57,10 +57,26 @@

 #' ## function makes sure that the region coordinates (chr, ranges, strand)

 #' ## of all samples are ordered correctly

 #'

-#'

 #' 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

+#' 

+#' sorted_grl_full <- 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

+#' 

+#' sorted_grl_full_except <- sort(grl)

+#' filter_and_extract(

+#'  sorted_grl_full_except, 

+#'  region_attributes = FULL("jaccard", "score")

+#' )

+#' 

 #' @export

 #'

 filter_and_extract <- function(

@@ -147,8 +163,7 @@ filter_and_extract <- function(

       vector_field, 

       samples_to_read, 

       regions,

-      suffix_vec,

-      vector_field

+      suffix_vec

     )

   } else {

@@ -362,6 +377,24 @@ filter_and_extract <- function(

   col_names <- names(df)

   df <- subset(df, TRUE, c("chr", "left", "right", "strand"))

+  # check if we used a FULL parameter instead of char array containing

+  # the region parameters

+  if(is.object(regions) && ("FULL" %in% class(regions))) {

+    all_values <- vector_field[!vector_field %in% c(

+      "chr", 

+      "left", 

+      "right",

+      "strand"

+      )

+    ]

+    except_values <- regions$values

+    regions <- if (is.null(except_values))

+      all_values

+    else

+      all_values[!all_values %in% except_values]

+    names(regions) <- NULL

+  }

+  

   if (!is.null(regions)) {

     df_list <- lapply(gdm_region_files, function(x, regions, vector_field) {

       region_frame <- data.table::fread(