@@ -3,28 +3,28 @@

 #########################

 DISTAL <- function(value) {

-  op_list <- list(value = value)

-  ## Set the name for the class

-  class(op_list) <- "DISTAL"

-  return(op_list)

+    op_list <- list(value = value)

+    ## Set the name for the class

+    class(op_list) <- "DISTAL"

+    return(op_list)

 }

 print.DISTAL <- function(obj) {

-  print(as.character.DISTAL(obj))

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

 }

 as.character.DISTAL <- function(obj) {

-  class <- class(obj)[1]

-  val <- obj$value

-  c(class,val)

+    class <- class(obj)[1]

+    val <- obj$value

+    c(class,val)

 }

 check.DISTAL <- function(value) {

-  if(!is.numeric(value))

-    stop("value: is not a numeric")

-  

-  if(is.numeric(value) && length(value)>1)

-    stop("value: no multiple string")

+    if(!is.numeric(value))

+        stop("value: is not a numeric")

+    

+    if(is.numeric(value) && length(value)>1)

+        stop("value: no multiple string")

 }

 #' DISTAL object class constructor

 #'

@@ -114,11 +114,11 @@ check.DISTAL <- function(value) {

 #' @export

 #' 

 DL <- function(value) {

-  check.DISTAL(value)

-  list <- list(value = as.integer(value))

-  ## Set the name for the class

-  class(list) <- c("DL","DISTAL")

-  return(list)

+    check.DISTAL(value)

+    list <- list(value = as.integer(value))

+    ## Set the name for the class

+    class(list) <- c("DL","DISTAL")

+    return(list)

 }

 #' @name DG

@@ -127,11 +127,11 @@ DL <- function(value) {

 #' @export

 #' 

 DG <- function(value) {

-  check.DISTAL(value)

-  list <- list(value = as.integer(value))

-  ## Set the name for the class

-  class(list) <- c("DG","DISTAL")

-  return(list)

+    check.DISTAL(value)

+    list <- list(value = as.integer(value))

+    ## Set the name for the class

+    class(list) <- c("DG","DISTAL")

+    return(list)

 }

 #' @name DISTAL-Object

@@ -140,11 +140,11 @@ DG <- function(value) {

 #' @export

 #' 

 DLE <- function(value) {

-  check.DISTAL(value)

-  list <- list(value = as.integer(value))

-  ## Set the name for the class

-  class(list) <- c("DLE","DISTAL")

-  return(list)

+    check.DISTAL(value)

+    list <- list(value = as.integer(value))

+    ## Set the name for the class

+    class(list) <- c("DLE","DISTAL")

+    return(list)

 }

 #' @name DISTAL-Object

@@ -153,11 +153,11 @@ DLE <- function(value) {

 #' @export

 #' 

 DGE <- function(value) {

-  check.DISTAL(value)

-  list <- list(value = as.integer(value))

-  ## Set the name for the class

-  class(list) <- c("DGE","DISTAL")

-  return(list)

+    check.DISTAL(value)

+    list <- list(value = as.integer(value))

+    ## Set the name for the class

+    class(list) <- c("DGE","DISTAL")

+    return(list)

 }

 #' @name DISTAL-Object

@@ -166,11 +166,11 @@ DGE <- function(value) {

 #' @export

 #' 

 MD <- function(value) {

-  check.DISTAL(value)

-  list <- list(value = as.integer(value))

-  ## Set the name for the class

-  class(list) <- c("MD","DISTAL")

-  return(list)

+    check.DISTAL(value)

+    list <- list(value = as.integer(value))

+    ## Set the name for the class

+    class(list) <- c("MD","DISTAL")

+    return(list)

 }

@@ -180,14 +180,14 @@ MD <- function(value) {

 #' @export

 #' 

 UP <- function() {

-  list <- list()

-  ## Set the name for the class

-  class(list) <- c("UP","DISTAL")

-  return(list)

+    list <- list()

+    ## Set the name for the class

+    class(list) <- c("UP","DISTAL")

+    return(list)

 }

 as.character.UP <- function(obj) {

-  class <- class(obj)[1]

-  c(class,"")

+    class <- class(obj)[1]

+    c(class,"")

 }

@@ -197,13 +197,13 @@ as.character.UP <- function(obj) {

 #' @export

 #' 

 DOWN <- function() {

-  list <- list()

-  ## Set the name for the class

-  class(list) <- c("DOWN","DISTAL")

-  return(list)

+    list <- list()

+    ## Set the name for the class

+    class(list) <- c("DOWN","DISTAL")

+    return(list)

 }

 as.character.DOWN <- function(obj) {

-  class <- class(obj)[1]

-  c(class,"")

+    class <- class(obj)[1]

+    c(class,"")

 }

old mode 100644

new mode 100755

@@ -2,31 +2,29 @@

 #       DISTAL          #

 #########################

-DISTAL <- function(value)

-{

-    op_list <- list(value = value)

-    ## Set the name for the class

-    class(op_list) <- "DISTAL"

-    return(op_list)

+DISTAL <- function(value) {

+  op_list <- list(value = value)

+  ## Set the name for the class

+  class(op_list) <- "DISTAL"

+  return(op_list)

 }

 print.DISTAL <- function(obj) {

-    print(as.character.DISTAL(obj))

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

 }

 as.character.DISTAL <- function(obj) {

-    class <- class(obj)[1]

-    val <- obj$value

-    c(class,val)

+  class <- class(obj)[1]

+  val <- obj$value

+  c(class,val)

 }

-check.DISTAL <- function(value)

-{

-    if(!is.numeric(value))

-        stop("value: is not a numeric")

-    

-    if(is.numeric(value) && length(value)>1)

-        stop("value: no multiple string")

+check.DISTAL <- function(value) {

+  if(!is.numeric(value))

+    stop("value: is not a numeric")

+  

+  if(is.numeric(value) && length(value)>1)

+    stop("value: no multiple string")

 }

 #' DISTAL object class constructor

 #'

@@ -115,13 +113,12 @@ check.DISTAL <- function(value)

 #' @rdname distal-class

 #' @export

 #' 

-DL <- function(value)

-{

-    check.DISTAL(value)

-    list <- list(value = as.integer(value))

-    ## Set the name for the class

-    class(list) <- c("DL","DISTAL")

-    return(list)

+DL <- function(value) {

+  check.DISTAL(value)

+  list <- list(value = as.integer(value))

+  ## Set the name for the class

+  class(list) <- c("DL","DISTAL")

+  return(list)

 }

 #' @name DG

@@ -129,13 +126,12 @@ DL <- function(value)

 #' @rdname distal-class

 #' @export

 #' 

-DG <- function(value)

-{

-    check.DISTAL(value)

-    list <- list(value = as.integer(value))

-    ## Set the name for the class

-    class(list) <- c("DG","DISTAL")

-    return(list)

+DG <- function(value) {

+  check.DISTAL(value)

+  list <- list(value = as.integer(value))

+  ## Set the name for the class

+  class(list) <- c("DG","DISTAL")

+  return(list)

 }

 #' @name DISTAL-Object

@@ -143,13 +139,12 @@ DG <- function(value)

 #' @rdname distal-class

 #' @export

 #' 

-DLE <- function(value)

-{

-    check.DISTAL(value)

-    list <- list(value = as.integer(value))

-    ## Set the name for the class

-    class(list) <- c("DLE","DISTAL")

-    return(list)

+DLE <- function(value) {

+  check.DISTAL(value)

+  list <- list(value = as.integer(value))

+  ## Set the name for the class

+  class(list) <- c("DLE","DISTAL")

+  return(list)

 }

 #' @name DISTAL-Object

@@ -157,13 +152,12 @@ DLE <- function(value)

 #' @rdname distal-class

 #' @export

 #' 

-DGE <- function(value)

-{

-    check.DISTAL(value)

-    list <- list(value = as.integer(value))

-    ## Set the name for the class

-    class(list) <- c("DGE","DISTAL")

-    return(list)

+DGE <- function(value) {

+  check.DISTAL(value)

+  list <- list(value = as.integer(value))

+  ## Set the name for the class

+  class(list) <- c("DGE","DISTAL")

+  return(list)

 }

 #' @name DISTAL-Object

@@ -171,13 +165,12 @@ DGE <- function(value)

 #' @rdname distal-class

 #' @export

 #' 

-MD <- function(value)

-{

-    check.DISTAL(value)

-    list <- list(value = as.integer(value))

-    ## Set the name for the class

-    class(list) <- c("MD","DISTAL")

-    return(list)

+MD <- function(value) {

+  check.DISTAL(value)

+  list <- list(value = as.integer(value))

+  ## Set the name for the class

+  class(list) <- c("MD","DISTAL")

+  return(list)

 }

@@ -186,16 +179,15 @@ MD <- function(value)

 #' @rdname distal-class

 #' @export

 #' 

-UP <- function()

-{

-    list <- list()

-    ## Set the name for the class

-    class(list) <- c("UP","DISTAL")

-    return(list)

+UP <- function() {

+  list <- list()

+  ## Set the name for the class

+  class(list) <- c("UP","DISTAL")

+  return(list)

 }

 as.character.UP <- function(obj) {

-    class <- class(obj)[1]

-    c(class,"")

+  class <- class(obj)[1]

+  c(class,"")

 }

@@ -204,17 +196,14 @@ as.character.UP <- function(obj) {

 #' @rdname distal-class

 #' @export

 #' 

-DOWN <- function()

-{

-    list <- list()

-    ## Set the name for the class

-    class(list) <- c("DOWN","DISTAL")

-    return(list)

+DOWN <- function() {

+  list <- list()

+  ## Set the name for the class

+  class(list) <- c("DOWN","DISTAL")

+  return(list)

 }

-

-

 as.character.DOWN <- function(obj) {

-    class <- class(obj)[1]

-    c(class,"")

+  class <- class(obj)[1]

+  c(class,"")

 }

@@ -80,7 +80,7 @@ check.DISTAL <- function(value)

 #' ## and creation of results on disk. Then, with system.file() it defines 

 #' ## the path to the folders "DATASET" and "DATASET_GDM" in the subdirectory 

 #' ## "example" of the package "RGMQL", and opens such folders as a GMQL 

-#' ## datasets named "TSS" and "HM", respectively, using customParser

+#' ## datasets named "TSS" and "HM", respectively, using CustomParser

 #' 

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

@@ -96,8 +96,8 @@ check.DISTAL <- function(value)

 #' ## samples are obtained from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

-#' genometric_predicate = list(MD(1), DL(1200)), conds("provider"), 

-#' region_output = "RIGHT")

+#'     genometric_predicate = list(MD(1), DL(1200)), conds("provider"), 

+#'     region_output = "RIGHT")

 #'

 #' ## Given a dataset HM and one called TSS with a sample including 

 #' ## Transcription Start Site annotations, this statement searches for those 

@@ -107,8 +107,8 @@ check.DISTAL <- function(value)

 #' ## TSS and HM samples are obtained from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

-#' genometric_predicate = list(MD(1), DGE(12000), DOWN()), conds("provider"), 

-#' region_output = "RIGHT")

+#'     genometric_predicate = list(MD(1), DGE(12000), DOWN()), 

+#'     conds("provider"), region_output = "RIGHT")

 #'

 #' @name DISTAL-Object

 #' @aliases DL

@@ -37,74 +37,74 @@ check.DISTAL <- function(value)

 #' \itemize{

 #' \item{DL: It denotes the less distance clause, 

 #' which selects all the regions of a joined experiment dataset sample such 

-#' that their distance from the anchor region of a joined reference dataset 

+#' that their distance from the anchor region of the joined reference dataset 

 #' sample is less than 'value' bases.}

-#' \item{DLE: It denotes the less distance clause, 

+#' \item{DLE: It denotes the less equal distance clause, 

 #' which selects all the regions of a joined experiment dataset sample such 

-#' that their distance from the anchor region of a joined reference dataset 

+#' that their distance from the anchor region of the joined reference dataset 

 #' sample is less than, or equal to, 'value' bases.}

-#' \item{DG: It denotes the less distance clause, 

+#' \item{DG: It denotes the great distance clause, 

 #' which selects all the regions of a joined experiment dataset sample such 

-#' that their distance from the anchor region of a joined reference dataset 

+#' that their distance from the anchor region of the joined reference dataset 

 #' sample is greater than 'value' bases. }

-#' \item{DGE: It denotes the less distance clause, 

+#' \item{DGE: It denotes the great equal distance clause, 

 #' which selects all the regions of a joined experiment dataset sample such 

-#' that their distance from the anchor region of a joined reference dataset 

+#' that their distance from the anchor region of the joined reference dataset 

 #' sample is greater than, or equal to, 'value' bases.}

 #' \item{MD: It denotes the minimum distance clause, which selects 

-#' the first 'value' regions of a joined experiment at minimial distance 

-#' from the anchor region of a joined reference dataset sample.}

+#' the first 'value' regions of the joined experiment at minimial distance 

+#' from the anchor region of the joined reference dataset sample.}

 #' \item{UP: It denotes the upstream direction of the genome.

-#' It makes predicates to be hold on the upstream of the regions of a joined 

-#' experiment dataset sample.

-#' UP is true when region of a joined experiment dataset sample is in the

-#' upstream genome of the anchor region of a joined reference dataset sample.

+#' It makes predicates to be hold on the upstream of the regions of the joined 

+#' reference dataset sample.

+#' UP is true when region of the joined experiment dataset sample is in the

+#' upstream genome of the anchor region of the joined reference dataset sample.

 #' When this clause is not present, distal conditions apply to both 

 #' directions of the genome.}

 #' \item{DOWN:  It denotes the downstream direction of the genome.

-#' It makes predicates to be hold on the downstream of the regions of a joined 

-#' experiment dataset sample.

-#' UP is true when region of a joined experiment dataset sample is in the

-#' downstream genome of the anchor region of a joined reference dataset sample.

-#' When this clause is not present, distal conditions apply to both 

+#' It makes predicates to be hold on the downstream of the regions of the 

+#' joined reference dataset sample.

+#' DOWN is true when region of the joined experiment dataset sample is in the

+#' downstream genome of the anchor region of the joined reference dataset 

+#' sample. When this clause is not present, distal conditions apply to both 

 #' directions of the genome.}

 #' }

 #' 

 #' @param value string identifying distance between genomic regions 

-#' in base pair, 

+#' in base pair

 #'

 #' @return Distal object

 #' 

 #' @examples

-#' ## Thi statement initializes and runs the GMQL server for local execution 

+#' ## This statement initializes and runs the GMQL server for local execution 

 #' ## and creation of results on disk. Then, with system.file() it defines 

 #' ## the path to the folders "DATASET" and "DATASET_GDM" in the subdirectory 

-#' ## "example" of the package "RGMQL" and opens such folder as a GMQL 

-#' ## dataset named "TSS" and "HM" respectively using customParser

+#' ## "example" of the package "RGMQL", and opens such folders as a GMQL 

+#' ## datasets named "TSS" and "HM", respectively, using customParser

 #' 

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

 #' test_path2 <- system.file("example", "DATASET_GDM", package = "RGMQL")

-#' TSS = read_GMQL(test_path)

-#' HM = read_GMQL(test_path2)

+#' TSS = read_gmql(test_path)

+#' HM = read_gmql(test_path2)

 #' 

 #' ## Given a dataset HM and one called TSS with a sample including 

-#' ## Transcription Start Site annotations, it searches for those regions of HM 

-#' ## that are at a minimal distance from a transcription start site (TSS) 

-#' ## and takes the first/closest one for each TSS, provided that such 

-#' ## distance is lesser than 1200 bases and joined TSS and HM samples are 

-#' ## obtained from the same provider (joinby clause).

+#' ## Transcription Start Site annotations, this statement  searches for those 

+#' ## regions of HM that are at a minimal distance from a transcription 

+#' ## start site (TSS) and takes the first/closest one for each TSS, provided 

+#' ## that such distance is lesser than 1200 bases and joined TSS and HM 

+#' ## samples are obtained from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

 #' genometric_predicate = list(MD(1), DL(1200)), conds("provider"), 

 #' region_output = "RIGHT")

 #'

-#' ## Given a dataset 'HM' and one called 'TSS' with a sample including 

-#' ## Transcription Start Site annotations, it searches for those regions of HM 

-#' ## that are at a minimal distance from a transcription start site (TSS) 

-#' ## and takes the first/closest one for each TSS, provided that such distance 

-#' ## is greater than 12K bases and joined 'tss' and 'hm' samples are obtained 

-#' ## from the same provider (joinby clause).

+#' ## Given a dataset HM and one called TSS with a sample including 

+#' ## Transcription Start Site annotations, this statement searches for those 

+#' ## regions of HM that are downstream and at a minimal distance from a 

+#' ## transcription start site (TSS) and takes the first/closest one for each 

+#' ## TSS, provided that such distance is greater than 12K bases and joined 

+#' ## TSS and HM samples are obtained from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

 #' genometric_predicate = list(MD(1), DGE(12000), DOWN()), conds("provider"), 

@@ -85,8 +85,8 @@ check.DISTAL <- function(value)

 #' init_gmql()

 #' test_path <- system.file("example", "DATASET", package = "RGMQL")

 #' test_path2 <- system.file("example", "DATASET_GDM", package = "RGMQL")

-#' TSS = read_dataset(test_path)

-#' HM = read_dataset(test_path2)

+#' TSS = read_GMQL(test_path)

+#' HM = read_GMQL(test_path2)

 #' 

 #' ## Given a dataset HM and one called TSS with a sample including 

 #' ## Transcription Start Site annotations, it searches for those regions of HM 

@@ -96,7 +96,7 @@ check.DISTAL <- function(value)

 #' ## obtained from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

-#' genometric_predicate = list(MD(1), DL(1200)), DF("provider"), 

+#' genometric_predicate = list(MD(1), DL(1200)), conds("provider"), 

 #' region_output = "RIGHT")

 #'

 #' ## Given a dataset 'HM' and one called 'TSS' with a sample including 

@@ -107,8 +107,8 @@ check.DISTAL <- function(value)

 #' ## from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

-#' genometric_predicate = list(MD(1), DGE(12000), DOWN()), 

-#' DF("provider"), region_output = "RIGHT")

+#' genometric_predicate = list(MD(1), DGE(12000), DOWN()), conds("provider"), 

+#' region_output = "RIGHT")

 #'

 #' @name DISTAL-Object

 #' @aliases DL

@@ -31,71 +31,80 @@ check.DISTAL <- function(value)

 #' DISTAL object class constructor

 #'

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

-#' to be used in GMQL functions that use genometric predicate parameter

-#' requiring distal condition on value

+#' to be used in GMQL JOIN operations (RGMQL merge functions) that use 

+#' genometric predicate parameter requiring distal condition on value

 #' 

 #' \itemize{

 #' \item{DL: It denotes the less distance clause, 

-#' which selects all the regions of the experiment such that their distance 

-#' from the anchor region is less than 'value' bases.}

+#' which selects all the regions of a joined experiment dataset sample such 

+#' that their distance from the anchor region of a joined reference dataset 

+#' sample is less than 'value' bases.}

 #' \item{DLE: It denotes the less distance clause, 

-#' which selects all the regions of the experiment such that their distance 

-#' from the anchor region is less than, or equal to, 'value' bases.}

-#' \item{DG: it denotes the less distance clause, 

-#' which selects all the regions of the experiment such that their distance 

-#' from the anchor region is greater than 'value' bases. }

-#' \item{DGE: It denotes the less distance clause, which selects all the 

-#' regions of the experiment such that their distance from the anchor region 

-#' is greater than, or equal to, 'value' bases.}

+#' which selects all the regions of a joined experiment dataset sample such 

+#' that their distance from the anchor region of a joined reference dataset 

+#' sample is less than, or equal to, 'value' bases.}

+#' \item{DG: It denotes the less distance clause, 

+#' which selects all the regions of a joined experiment dataset sample such 

+#' that their distance from the anchor region of a joined reference dataset 

+#' sample is greater than 'value' bases. }

+#' \item{DGE: It denotes the less distance clause, 

+#' which selects all the regions of a joined experiment dataset sample such 

+#' that their distance from the anchor region of a joined reference dataset 

+#' sample is greater than, or equal to, 'value' bases.}

 #' \item{MD: It denotes the minimum distance clause, which selects 

-#' the 'value' regions of the experiment at minimial distance from the 

-#' anchor region.}

+#' the first 'value' regions of a joined experiment at minimial distance 

+#' from the anchor region of a joined reference dataset sample.}

 #' \item{UP: It denotes the upstream direction of the genome.

-#' They are interpreted as predicates that must hold on the regions 

-#' of the experiment.

-#' UP is true when region of experiment is in the upstream genome 

-#' of the anchor region.

+#' It makes predicates to be hold on the upstream of the regions of a joined 

+#' experiment dataset sample.

+#' UP is true when region of a joined experiment dataset sample is in the

+#' upstream genome of the anchor region of a joined reference dataset sample.

 #' When this clause is not present, distal conditions apply to both 

-#' the directions of the genome.}

-#' \item{DOWN: It denotes the downstream direction of the genome.

-#' They are interpreted as predicates that must hold on the regions of 

-#' the experiment.

-#' DOWN is true when region of experiment is in the downstream genome of 

-#' the anchor region.

-#' When this clause is not present, distal conditions apply to both the 

-#' directions of the genome. }

+#' directions of the genome.}

+#' \item{DOWN:  It denotes the downstream direction of the genome.

+#' It makes predicates to be hold on the downstream of the regions of a joined 

+#' experiment dataset sample.

+#' UP is true when region of a joined experiment dataset sample is in the

+#' downstream genome of the anchor region of a joined reference dataset sample.

+#' When this clause is not present, distal conditions apply to both 

+#' directions of the genome.}

 #' }

 #' 

 #' @param value string identifying distance between genomic regions 

-#' in base pairs, 

+#' in base pair, 

 #'

-#' @return distal object

+#' @return Distal object

 #' 

 #' @examples

+#' ## Thi statement initializes and runs the GMQL server for local execution 

+#' ## and creation of results on disk. Then, with system.file() it defines 

+#' ## the path to the folders "DATASET" and "DATASET_GDM" in the subdirectory 

+#' ## "example" of the package "RGMQL" and opens such folder as a GMQL 

+#' ## dataset named "TSS" and "HM" respectively using customParser

 #' 

 #' init_gmql()

-#' test_path <- system.file("example","DATASET",package = "RGMQL")

-#' test_path2 <- system.file("example","DATASET_GDM",package = "RGMQL")

+#' test_path <- system.file("example", "DATASET", package = "RGMQL")

+#' test_path2 <- system.file("example", "DATASET_GDM", package = "RGMQL")

 #' TSS = read_dataset(test_path)

 #' HM = read_dataset(test_path2)

 #' 

 #' ## Given a dataset HM and one called TSS with a sample including 

-#' # Transcription Start Site annotations, it searches for those regions of hm 

-#' # that are at a minimal distance from a transcription start site (TSS) 

-#' # and takes the first/closest one for each TSS, 

-#' # provided that such distance is lesser than 1200 bases and joined TSS 

-#' # and HM samples are obtained from the same provider (joinby clause).

+#' ## Transcription Start Site annotations, it searches for those regions of HM 

+#' ## that are at a minimal distance from a transcription start site (TSS) 

+#' ## and takes the first/closest one for each TSS, provided that such 

+#' ## distance is lesser than 1200 bases and joined TSS and HM samples are 

+#' ## obtained from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

 #' genometric_predicate = list(MD(1), DL(1200)), DF("provider"), 

 #' region_output = "RIGHT")

 #'

-#' #' # Given a dataset 'hm' and one called 'tss' with a sample including 

-#' # Transcription Start Site annotations, it searches for those regions of hm 

-#' # that are at a minimal distance from a transcription start site (TSS) 

-#' # and takes the first/closest one for each TSS, provided that such distance 

-#' # is greater than 12K bases and joined 'tss' and 'hm' samples are obtained 

-#' # from the same provider (joinby clause).

+#' ## Given a dataset 'HM' and one called 'TSS' with a sample including 

+#' ## Transcription Start Site annotations, it searches for those regions of HM 

+#' ## that are at a minimal distance from a transcription start site (TSS) 

+#' ## and takes the first/closest one for each TSS, provided that such distance 

+#' ## is greater than 12K bases and joined 'tss' and 'hm' samples are obtained 

+#' ## from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

 #' genometric_predicate = list(MD(1), DGE(12000), DOWN()), 

@@ -101,7 +101,7 @@ check.DISTAL <- function(value)

 #' genometric_predicate = list(MD(1), DGE(12000), DOWN()), 

 #' DF("provider"), region_output = "RIGHT")

 #'

-#' @name DL

+#' @name DISTAL-Object

 #' @aliases DL

 #' @rdname distal-class

 #' @export

@@ -129,7 +129,7 @@ DG <- function(value)

     return(list)

 }

-#' @name DLE

+#' @name DISTAL-Object

 #' @aliases DLE

 #' @rdname distal-class

 #' @export

@@ -143,7 +143,7 @@ DLE <- function(value)

     return(list)

 }

-#' @name DGE

+#' @name DISTAL-Object

 #' @aliases DGE

 #' @rdname distal-class

 #' @export

@@ -157,7 +157,7 @@ DGE <- function(value)

     return(list)

 }

-#' @name MD

+#' @name DISTAL-Object

 #' @aliases MD

 #' @rdname distal-class

 #' @export

@@ -172,7 +172,7 @@ MD <- function(value)

 }

-#' @name UP

+#' @name DISTAL-Object

 #' @aliases UP

 #' @rdname distal-class

 #' @export

@@ -190,7 +190,7 @@ as.character.UP <- function(obj) {

 }

-#' @name DOWN

+#' @name DISTAL-Object

 #' @aliases DOWN

 #' @rdname distal-class

 #' @export

@@ -87,7 +87,7 @@ check.DISTAL <- function(value)

 #' # and HM samples are obtained from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

-#' genometric_predicate = list(list(MD(1), DL(1200))), DF("provider"), 

+#' genometric_predicate = list(MD(1), DL(1200)), DF("provider"), 

 #' region_output = "RIGHT")

 #'

 #' #' # Given a dataset 'hm' and one called 'tss' with a sample including 

@@ -98,7 +98,7 @@ check.DISTAL <- function(value)

 #' # from the same provider (joinby clause).

 #' 

 #' join_data = merge(TSS, HM, 

-#' genometric_predicate = list(list(MD(1), DGE(12000), DOWN())), 

+#' genometric_predicate = list(MD(1), DGE(12000), DOWN()), 

 #' DF("provider"), region_output = "RIGHT")

 #'

 #' @name DL

@@ -101,7 +101,8 @@ check.DISTAL <- function(value)

 #' genometric_predicate = list(list(MD(1), DGE(12000), DOWN())), 

 #' DF("provider"), region_output = "RIGHT")

 #'

-#' @name DISTAL

+#' @name DL

+#' @aliases DL

 #' @rdname distal-class

 #' @export

 #' 

@@ -114,7 +115,8 @@ DL <- function(value)

     return(list)

 }

-#' @name DISTAL

+#' @name DG

+#' @aliases DG

 #' @rdname distal-class

 #' @export

 #' 

@@ -127,7 +129,8 @@ DG <- function(value)

     return(list)

 }

-#' @name DISTAL

+#' @name DLE

+#' @aliases DLE

 #' @rdname distal-class

 #' @export

 #' 

@@ -140,7 +143,8 @@ DLE <- function(value)

     return(list)

 }

-#' @name DISTAL

+#' @name DGE

+#' @aliases DGE

 #' @rdname distal-class

 #' @export

 #' 

@@ -153,7 +157,8 @@ DGE <- function(value)

     return(list)

 }

-#' @name DISTAL

+#' @name MD

+#' @aliases MD

 #' @rdname distal-class

 #' @export

 #' 

@@ -167,7 +172,8 @@ MD <- function(value)

 }

-#' @name DISTAL

+#' @name UP

+#' @aliases UP

 #' @rdname distal-class

 #' @export

 #' 

@@ -184,7 +190,8 @@ as.character.UP <- function(obj) {

 }

-#' @name DISTAL

+#' @name DOWN

+#' @aliases DOWN

 #' @rdname distal-class

 #' @export

 #' 

new file mode 100644

@@ -0,0 +1,204 @@

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

+#       DISTAL          #

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

+

+DISTAL <- function(value)

+{

+    op_list <- list(value = value)

+    ## Set the name for the class

+    class(op_list) <- "DISTAL"

+    return(op_list)

+}

+

+print.DISTAL <- function(obj) {

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

+}

+

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

+    class <- class(obj)[1]

+    val <- obj$value

+    c(class,val)

+}

+

+check.DISTAL <- function(value)

+{

+    if(!is.numeric(value))

+        stop("value: is not a numeric")

+    

+    if(is.numeric(value) && length(value)>1)

+        stop("value: no multiple string")

+}

+#' DISTAL object class constructor

+#'

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

+#' to be used in GMQL functions that use genometric predicate parameter

+#' requiring distal condition on value

+#' 

+#' \itemize{

+#' \item{DL: It denotes the less distance clause, 

+#' which selects all the regions of the experiment such that their distance 

+#' from the anchor region is less than 'value' bases.}

+#' \item{DLE: It denotes the less distance clause, 

+#' which selects all the regions of the experiment such that their distance 

+#' from the anchor region is less than, or equal to, 'value' bases.}

+#' \item{DG: it denotes the less distance clause, 

+#' which selects all the regions of the experiment such that their distance 

+#' from the anchor region is greater than 'value' bases. }

+#' \item{DGE: It denotes the less distance clause, which selects all the 

+#' regions of the experiment such that their distance from the anchor region 

+#' is greater than, or equal to, 'value' bases.}

+#' \item{MD: It denotes the minimum distance clause, which selects 

+#' the 'value' regions of the experiment at minimial distance from the 

+#' anchor region.}

+#' \item{UP: It denotes the upstream direction of the genome.

+#' They are interpreted as predicates that must hold on the regions 

+#' of the experiment.

+#' UP is true when region of experiment is in the upstream genome 

+#' of the anchor region.

+#' When this clause is not present, distal conditions apply to both 

+#' the directions of the genome.}

+#' \item{DOWN: It denotes the downstream direction of the genome.

+#' They are interpreted as predicates that must hold on the regions of 

+#' the experiment.

+#' DOWN is true when region of experiment is in the downstream genome of 

+#' the anchor region.

+#' When this clause is not present, distal conditions apply to both the 

+#' directions of the genome. }

+#' }

+#' 

+#' @param value string identifying distance between genomic regions 

+#' in base pairs, 

+#'

+#' @return distal object