1. RGMQL
  2. Commit 43d9e4a18e6a670ab22f4a35bde5d27dbbbb8dde
Browse code

passing to rJava

Simone authored on 16/10/2017 16:18:37
Showing 73 changed files
DESCRIPTION
History View file @ 43d9e4a
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: RGMQL
2 2 
 Type: Package
3 3 
 Title: GenoMetric Query Language for R/Bioconductor
4 
-Version: 0.99.2
4 
+Version: 0.99.3
5 5 
 Author: Simone Pallotta, Marco Masseroli
6 6 
 Maintainer: Simone Pallotta <simonepallotta@hotmail.com>
7 7 
 Description: This package brings GMQL functionalities into R environemnt.
NAMESPACE
History View file @ 43d9e4a
... ... 
@@ -1,30 +1,76 @@
1 1 
 # Generated by roxygen2: do not edit by hand
2 2
3 
+export(ASC)
4 
+export(AVG)
5 
+export(BAG)
6 
+export(COUNT)
7 
+export(DEF)
8 
+export(DESC)
9 
+export(DG)
10 
+export(DGE)
11 
+export(DL)
12 
+export(DLE)
13 
+export(DOWN)
14 
+export(EXACT)
15 
+export(FULL)
16 
+export(MAX)
17 
+export(MD)
18 
+export(MEDIAN)
19 
+export(MIN)
20 
+export(Q1)
21 
+export(Q2)
22 
+export(Q3)
23 
+export(STD)
24 
+export(SUM)
3 25 
 export(TFARMatrix)
4 26 
 export(TFARMemAtrix)
27 
+export(UP)
28 
+export(compileQuery)
29 
+export(compileQuery.fromfile)
30 
+export(cover)
5 31 
 export(deleteDataset)
32 
+export(difference)
6 33 
 export(downloadDataset)
7 34 
 export(downloadDatasetToGrangesList)
35 
+export(execute)
8 36 
 export(exportGMQL.gdm)
9 37 
 export(exportGMQL.gtf)
10 38 
 export(extend)
39 
+export(flat)
40 
+export(histogram)
11 41 
 export(importGMQL.gdm)
12 42 
 export(importGMQL.gtf)
13 43 
 export(initGMQL)
44 
+export(join)
14 45 
 export(login.GMQL)
15 46 
 export(logout.GMQL)
47 
+export(map)
48 
+export(materialize)
49 
+export(merge)
16 50 
 export(metadataFromSample)
51 
+export(order)
52 
+export(project)
17 53 
 export(read)
18 54 
 export(readDataset)
19 55 
 export(regionFromSample)
20 56 
 export(register.GMQL)
21 57 
 export(remote_processing)
58 
+export(runQuery)
59 
+export(runQuery.fromfile)
22 60 
 export(saveQuery)
23 61 
 export(saveQuery.fromfile)
62 
+export(select)
24 63 
 export(showDatasets)
64 
+export(showJobLog)
65 
+export(showJobs)
25 66 
 export(showQueries)
26 67 
 export(showSamplesFromDataset)
27 68 
 export(showSchemaFromDataset)
69 
+export(stopJob)
70 
+export(summit)
71 
+export(take)
72 
+export(traceJob)
73 
+export(union)
28 74 
 export(uploadSamples)
29 75 
 import(GenomicRanges)
30 76 
 import(httr)
... ... 
@@ -36,12 +82,15 @@ importFrom(data.table,fread)
36 82 
 importFrom(dplyr,bind_cols)
37 83 
 importFrom(methods,is)
38 84 
 importFrom(plyr,revalue)
85 
+importFrom(rJava,.jarray)
86 
+importFrom(rJava,.jevalArray)
39 87 
 importFrom(rJava,.jinit)
40 88 
 importFrom(rJava,.jnull)
41 89 
 importFrom(rJava,.jpackage)
42 90 
 importFrom(rJava,J)
43 91 
 importFrom(rtracklayer,export)
44 92 
 importFrom(rtracklayer,import)
93 
+importFrom(stats,setNames)
45 94 
 importFrom(utils,read.delim)
46 95 
 importFrom(utils,unzip)
47 96 
 importFrom(utils,write.table)
R/Cover.R
History View file @ 43d9e4a
48 97 
new file mode 100644
... ... 
@@ -0,0 +1,360 @@
1 
+#' GMQL Operation: COVER
2 
+#'
3 
+#' it takes as input a dataset and returns another dataset (with a single sample, if no \emph{groupby} option is specified)
4 
+#' by “collapsing” the input dataset samples and their regions according to certain rules specified by the input parameters.
5 
+#' The attributes of the output genomic regions are only the region coordinates, and Jaccard indexes (JaccardIntersect and JaccardResult).
6 
+#' Jaccard Indexes are standard measures of similarity of the contributing regions, added as default region attributes.
7 
+#' The JaccardIntersect index is calculated as the ratio between the lengths of the intersection
8 
+#' and of the union of the contributing regions; the JaccardResult index is calculated as the ratio
9 
+#' between the lengths of region and the union of the contributing regions.
10 
+#' If aggregate functions are specified, new attributes are added.
11 
+#' Output metadata are the union of the input ones.
12 
+#' If \emph{groupby} clause is specified, the input samples are partitioned in groups,
13 
+#' each with distinct values of the grouping metadata attributes, and the COVER operation is separately
14 
+#' applied to each group, yielding to one sample in the result for each group.
15 
+#' Input samples that do not satisfy the \emph{groupby} condition are disregarded.
16 
+#'
17 
+#' @importFrom methods is
18 
+#' @importFrom rJava J
19 
+#' @importFrom rJava .jnull
20 
+#' @importFrom rJava .jarray
21 
+#'
22 
+#' @param input_data returned object from any GMQL function
23 
+#' @param minAcc minimum number of overlapping regions to be considered during executio.n
24 
+#' Is a single integer number, declared also as string.
25 
+#' minAcc accept ALL and string like (ALL+N)/K as special keyword
26 
+#' ALL sets the minimum to the number of samples in the input dataset
27 
+#' @param maxAcc maximum number of overlapping regions to be considered during execution.
28 
+#' Is a single integer number, declared also as string.
29 
+#' maxAcc accept ALL, ANY and string like (ALL+N)/K as special keyword
30 
+#' ALL sets the maximum to the number of samples in the input dataset
31 
+#' ANY acts as a wildcard, consider all areas defined to any amount of overlapping
32 
+#' @param groupBy list of CONDITION objects, or simple string concatenation
33 
+#' (i.e c("cell_type","attribute_tag","size")).
34 
+#' Every object contains the name of metadata to be used in \emph{groupby}.
35 
+#' For details of CONDITION objects see:
36 
+#' \code{\link{DEF}}, \code{\link{FULL}}, \code{\link{EXACT}}
37 
+#'
38 
+#' Every condition accepts only one string value. (e.g. DEF("cell_type") )
39 
+#' In case of single concatenation with no CONDITION, all metadata are considering as DEF
40 
+#'
41 
+#' @param aggregates list of element in the form \emph{key} = \emph{function_aggregate}.
42 
+#' The \emph{function_aggregate} is an object of class OPERATOR
43 
+#' The aggregate functions available are: \code{\link{MIN}}, \code{\link{MAX}},
44 
+#' \code{\link{SUM}}, \code{\link{BAG}}, \code{\link{AVG}}, \code{\link{COUNT}},
45 
+#' \code{\link{STD}}, \code{\link{MEDIAN}}, \code{\link{Q1}}, \code{\link{Q2}},
46 
+#' \code{\link{Q3}}.
47 
+#' Every operator accepts a string value, execet for COUNT that cannot have a value.
48 
+#' Argument of 'function_aggregate' must exist in schema
49 
+#' Two style are allowed:
50 
+#' \itemize{
51 
+#' \item list of key-value pairs: e.g. sum = SUM("pvalue")
52 
+#' \item list of values: e.g. SUM("pvalue")
53 
+#' }
54 
+#' "mixed style" is not allowed
55 
+#'
56 
+#' @return DAGgraph class object. It contains the value associated to the graph used
57 
+#' as input for the subsequent GMQL function
58 
+#'
59 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
60 
+#'
61 
+#' @seealso  \code{\link{summit}} \code{\link{flat}} \code{\link{histogram}}
62 
+#'
63 
+#' @examples
64 
+#'
65 
+#' ## This GMQL statement produces an output dataset with a single output sample.
66 
+#' ## The COVER operation considers all areas defined by a minimum of two overlapping regions
67 
+#' ## in the input samples, up to any amount of overlapping regions.
68 
+#'
69 
+#' initGMQL("gtf")
70 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
71 
+#' exp = readDataset(test_path)
72 
+#' res = cover(input_data = exp,2,"ANY")
73 
+#'
74 
+#' \dontrun{
75 
+#' ## This GMQL statement computes the result grouping the input exp samples by the values of
76 
+#' ## their cell metadata attribute,
77 
+#' ## thus one output res sample is generated for each cell type;
78 
+#' ## output regions are produced where at least 2 and at most 3 regions of grouped exp samples
79 
+#' ## overlap, setting as attributes of the resulting regions the minimum pvalue of the overlapping regions
80 
+#' ## (min_pvalue) and their Jaccard indexes (JaccardIntersect and JaccardResult).
81 
+#'
82 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
83 
+#' exp = read(test_path)
84 
+#' res = cover(input_data = exp,2,3, c("cell"), list(min_pValue = MIN("pvalue")))
85 
+#' }
86 
+#' @export
87 
+#'
88 
+cover <- function(input_data, minAcc, maxAcc, groupBy = NULL, aggregates = NULL)
89 
+{
90 
+  .doVariant("COVER",minAcc,maxAcc,groupBy,aggregates,input_data)
91 
+}
92 
+
93 
+#' GMQL Operation: HISTOGRAM
94 
+#'
95 
+#' returns the non-overlapping regions contributing to the cover,
96 
+#' each with its accumulation index value, which is assigned to the AccIndex region attribute.
97 
+#'
98 
+#' @importFrom methods is
99 
+#' @importFrom rJava J
100 
+#' @importFrom rJava .jnull
101 
+#' @importFrom rJava .jarray
102 
+#'
103 
+#' @param input_data returned object from any GMQL function
104 
+#' @param minAcc minimum number of overlapping regions to be considered during execution
105 
+#' normally is a single integer number, declared also as string.
106 
+#' minAcc accept ALL and string like (ALL+N)/K as special keyword
107 
+#' ALL sets the minimum to the number of samples in the input dataset
108 
+#' @param maxAcc maximum number of overlapping regions to be considered during execution
109 
+#' normally is a single integer number, declared also as string.
110 
+#' maxAcc accept ALL, ANY and string like (ALL+N)/K as special keyword
111 
+#' ALL sets the maximum to the number of samples in the input dataset
112 
+#' ANY acts as a wildcard, consider all areas defined to any amount of overlapping
113 
+#' @param groupBy list of CONDITION objects, or simple string concatenation
114 
+#' (i.e c("cell_type","attribute_tag","size")).
115 
+#' Every object contains the name of metadata to be used in \emph{groupby}.
116 
+#' For details of CONDITION objects see:
117 
+#' \code{\link{DEF}}, \code{\link{FULL}}, \code{\link{EXACT}}
118 
+#'
119 
+#' Every condition accepts only one string value. (e.g. DEF("cell_type") )
120 
+#' In case of single concatenation with no CONDITION, all metadata are considering as DEF
121 
+#'
122 
+#' @param aggregates list of element in the form \emph{key} = \emph{function_aggregate}.
123 
+#' The \emph{function_aggregate} is an object of class OPERATOR
124 
+#' The aggregate functions available are: \code{\link{MIN}}, \code{\link{MAX}},
125 
+#' \code{\link{SUM}}, \code{\link{BAG}}, \code{\link{AVG}}, \code{\link{COUNT}},
126 
+#' \code{\link{STD}}, \code{\link{MEDIAN}}, \code{\link{Q1}}, \code{\link{Q2}},
127 
+#' \code{\link{Q3}}.
128 
+#' Every operator accepts a string value, execet for COUNT that cannot have a value.
129 
+#' Argument of 'function_aggregate' must exist in schema
130 
+#' Two style are allowed:
131 
+#' \itemize{
132 
+#' \item list of key-value pairs: e.g. sum = SUM("pvalue")
133 
+#' \item list of values: e.g. SUM("pvalue")
134 
+#' }
135 
+#' "mixed style" is not allowed
136 
+#'
137 
+#' @return DAGgraph class object. It contains the value associated to the graph used
138 
+#' as input for the subsequent GMQL function
139 
+#'
140 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
141 
+#' @seealso \code{\link{flat}} \code{\link{cover}} \code{\link{summit}}
142 
+#'
143 
+#' @examples
144 
+#'
145 
+#' ## This GMQL statement computes the result grouping the input \emph{exp} samples
146 
+#' ## by the values of their \emph{cell} metadata attribute,
147 
+#' ## thus one output \emph{res} sample is generated for each cell type.
148 
+#' ## Output regions are produced by dividing results from COVER in contiguous subregions
149 
+#' ## according to the varying accumulation values (from 2 to 4 in this case):
150 
+#' ## one region for each accumulation value;
151 
+#'
152 
+#' initGMQL("gtf")
153 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
154 
+#' exp = readDataset(test_path)
155 
+#' res = histogram(exp, 2,4,groupBy = c("cell"))
156 
+#'
157 
+#' @export
158 
+#'
159 
+histogram <- function(input_data, minAcc, maxAcc, groupBy = NULL, aggregates = NULL)
160 
+{
161 
+  .doVariant("HISTOGRAM",minAcc,maxAcc,groupBy,aggregates,input_data)
162 
+}
163 
+
164 
+#' GMQL Operation: SUMMIT
165 
+#'
166 
+#' returns regions that start from a position
167 
+#' where the number of intersecting regions is not increasing afterwards and stops
168 
+#' at a position where either the number of intersecting regions decreases,
169 
+#' or it violates the max accumulation index).
170 
+#'
171 
+#' @importFrom methods is
172 
+#' @importFrom rJava J
173 
+#' @importFrom rJava .jnull
174 
+#' @importFrom rJava .jarray
175 
+#'
176 
+#' @param input_data returned object from any GMQL function
177 
+#' @param minAcc minimum number of overlapping regions to be considered during execution
178 
+#' normally is a single integer number, declared also as string.
179 
+#' minAcc accept ALL and string like (ALL+N)/K as special keyword
180 
+#' ALL sets the minimum to the number of samples in the input dataset
181 
+#' @param maxAcc maximum number of overlapping regions to be considered during execution
182 
+#' normally is a single integer number, declared also as string.
183 
+#' maxAcc accept ALL, ANY and string like (ALL+N)/K as special keyword
184 
+#' ALL sets the maximum to the number of samples in the input dataset
185 
+#' ANY acts as a wildcard, consider all areas defined to any amount of overlapping
186 
+#' @param groupBy list of CONDITION objects, or simple string concatenation
187 
+#' (i.e c("cell_type","attribute_tag","size")).
188 
+#' Every object contains the name of metadata to be used in \emph{groupby}.
189 
+#' For details of CONDITION objects see:
190 
+#' \code{\link{DEF}}, \code{\link{FULL}}, \code{\link{EXACT}}
191 
+#'
192 
+#' Every condition accepts only one string value. (e.g. DEF("cell_type") )
193 
+#' In case of single concatenation with no CONDITION, all metadata are considering as DEF
194 
+#'
195 
+#' @param aggregates list of element in the form \emph{key} = \emph{function_aggregate}.
196 
+#' The \emph{function_aggregate} is an object of class OPERATOR
197 
+#' The aggregate functions available are: \code{\link{MIN}}, \code{\link{MAX}},
198 
+#' \code{\link{SUM}}, \code{\link{BAG}}, \code{\link{AVG}}, \code{\link{COUNT}},
199 
+#' \code{\link{STD}}, \code{\link{MEDIAN}}, \code{\link{Q1}}, \code{\link{Q2}},
200 
+#' \code{\link{Q3}}.
201 
+#' Every operator accepts a string value, execet for COUNT that cannot have a value.
202 
+#' Argument of 'function_aggregate' must exist in schema
203 
+#' Two style are allowed:
204 
+#' \itemize{
205 
+#' \item list of key-value pairs: e.g. sum = SUM("pvalue")
206 
+#' \item list of values: e.g. SUM("pvalue")
207 
+#' }
208 
+#' "mixed style" is not allowed
209 
+#'
210 
+#' @return DAGgraph class object. It contains the value associated to the graph used
211 
+#' as input for the subsequent GMQL function
212 
+#'
213 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
214 
+#' @seealso \code{\link{flat}} \code{\link{cover}} \code{\link{histogram}}
215 
+#'
216 
+#' @examples
217 
+#'
218 
+#' ## This GMQL statement computes the result grouping the input \emph{exp} samples by the values
219 
+#' ## of their \emph{cell} metadata attribute, thus one output \emph{res} sample is generated
220 
+#' ## for each cell type.
221 
+#' ## Output regions are produced by extracting the highest accumulation overlapping
222 
+#' ## (sub)regions according to the methodologies described above;
223 
+#'
224 
+#'
225 
+#' initGMQL("gtf")
226 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
227 
+#' exp = readDataset(test_path)
228 
+#' res = summit(input_data = exp,2,4, c("cell"))
229 
+#'
230 
+#' @export
231 
+#'
232 
+summit <- function(input_data, minAcc, maxAcc, groupBy = NULL, aggregates = NULL)
233 
+{
234 
+  .doVariant("SUMMIT",minAcc,maxAcc,groupBy,aggregates,input_data)
235 
+}
236 
+
237 
+#' GMQL Operation: FLAT
238 
+#'
239 
+#' returns the contiguous region that starts from the first end and stops at
240 
+#' the last end of the regions which would contribute to each region of the COVER
241 
+#'
242 
+#' @importFrom methods is
243 
+#' @importFrom rJava J
244 
+#' @importFrom rJava .jnull
245 
+#' @importFrom rJava .jarray
246 
+#'
247 
+#' @param input_data returned object from any GMQL function
248 
+#' @param minAcc minimum number of overlapping regions to be considered during execution
249 
+#' normally is a single integer number, declared also as string.
250 
+#' minAcc accept ALL and string like (ALL+N)/K as special keyword
251 
+#' ALL sets the minimum to the number of samples in the input dataset
252 
+#' @param maxAcc maximum number of overlapping regions to be considered during execution
253 
+#' normally is a single integer number, declared also as string.
254 
+#' maxAcc accept ALL, ANY and string like (ALL+N)/K as special keyword
255 
+#' ALL sets the maximum to the number of samples in the input dataset
256 
+#' ANY acts as a wildcard, consider all areas defined to any amount of overlapping
257 
+#' @param groupBy list of CONDITION objects, or simple string concatenation
258 
+#' (i.e c("cell_type","attribute_tag","size")).
259 
+#' Every object contains the name of metadata to be used in \emph{groupBy}.
260 
+#' For details of CONDITION objects see:
261 
+#' \code{\link{DEF}}, \code{\link{FULL}}, \code{\link{EXACT}}
262 
+#'
263 
+#' Every condition accepts only one string value. (e.g. DEF("cell_type") )
264 
+#' In case of single concatenation with no CONDITION, all metadata are considering as DEF
265 
+#'
266 
+#' @param aggregates list of element in the form \emph{key} = \emph{function_aggregate}.
267 
+#' The \emph{function_aggregate} is an object of class OPERATOR
268 
+#' The aggregate functions available are: \code{\link{MIN}}, \code{\link{MAX}},
269 
+#' \code{\link{SUM}}, \code{\link{BAG}}, \code{\link{AVG}}, \code{\link{COUNT}},
270 
+#' \code{\link{STD}}, \code{\link{MEDIAN}}, \code{\link{Q1}}, \code{\link{Q2}},
271 
+#' \code{\link{Q3}}.
272 
+#' Every operator accepts a string value, execet for COUNT that cannot have a value.
273 
+#' Argument of 'function_aggregate' must exist in schema
274 
+#' Two style are allowed:
275 
+#' \itemize{
276 
+#' \item list of key-value pairs: e.g. sum = SUM("pvalue")
277 
+#' \item list of values: e.g. SUM("pvalue")
278 
+#' }
279 
+#' "mixed style" is not allowed
280 
+#'
281 
+#' @return DAGgraph class object. It contains the value associated to the graph used
282 
+#' as input for the subsequent GMQL function
283 
+#'
284 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
285 
+#' @seealso \code{\link{summit}} \code{\link{cover}} \code{\link{histogram}}
286 
+#'
287 
+#' @examples
288 
+#'
289 
+#' ## This GMQL statement computes the result grouping the input \emph{exp} samples by
290 
+#' ## the values of their \emph{cell} metadata attribute, thus one output \emph{res} sample
291 
+#' ## is generated for each cell type.
292 
+#' ## Output regions are produced by concatenating all regions which would have been used
293 
+#' ## to construct a COVER(2,4) statement on the same dataset;
294 
+#'
295 
+#' initGMQL("gtf")
296 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
297 
+#' exp = readDataset(test_path)
298 
+#' res = flat(input_data = exp,2,4, c("cell"))
299 
+#'
300 
+#' @export
301 
+#'
302 
+flat <- function(input_data, minAcc, maxAcc, groupBy = NULL, aggregates = NULL)
303 
+{
304 
+  .doVariant("FLAT",minAcc,maxAcc,groupBy,aggregates,input_data)
305 
+}
306 
+
307 
+.doVariant <- function(flag,minAcc,maxAcc,groupBy,aggregates,input_data)
308 
+{
309 
+  min <- .check_cover_param(minAcc,TRUE)
310 
+  max <- .check_cover_param(maxAcc,FALSE)
311 
+
312 
+  if(!is.null(groupBy))
313 
+    join_condition_matrix <- .jarray(.join_condition(groupBy),dispatch = TRUE)
314 
+  else
315 
+    join_condition_matrix <- .jnull("java/lang/String")
316 
+
317 
+  if(!is.null(aggregates))
318 
+    metadata_matrix <- .jarray(.aggregates(aggregates,"OPERATOR"),dispatch = TRUE)
319 
+  else
320 
+    metadata_matrix <- .jnull("java/lang/String")
321 
+
322 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
323 
+  response <- switch(flag,
324 
+                "COVER" = WrappeR$cover(min,max,join_condition_matrix,metadata_matrix,input_data$value),
325 
+                "FLAT" = WrappeR$flat(min,max,join_condition_matrix,metadata_matrix,input_data$value),
326 
+                "SUMMIT" = WrappeR$summit(min,max,join_condition_matrix,metadata_matrix,input_data$value),
327 
+                "HISTOGRAM" = WrappeR$histogram(min,max,join_condition_matrix,metadata_matrix,input_data$value))
328 
+
329 
+  error <- strtoi(response[1])
330 
+  data <- response[2]
331 
+
332 
+  if(error!=0)
333 
+    stop(data)
334 
+  else
335 
+    DAGgraph(data)
336 
+}
337 
+
338 
+.check_cover_param <- function(param,is_min)
339 
+{
340 
+  if(length(param)>1)
341 
+    stop("length > 1")
342 
+
343 
+  if(is.numeric(param))
344 
+  {
345 
+    if(param<=0)
346 
+      stop("No negative value")
347 
+    else
348 
+      return(as.character(param))
349 
+  }
350 
+  else if(is.character(param))
351 
+  {
352 
+    if(is_min && identical(param,"ANY"))
353 
+      stop("min cannot assume ANY as value")
354 
+    return(param)
355 
+  }
356 
+  else
357 
+    stop("invalid input data")
358 
+}
359 
+
360 
+
R/Difference.R
History View file @ 43d9e4a
0 361 
new file mode 100644
... ... 
@@ -0,0 +1,83 @@
1 
+#' GMQL Operation: DIFFERENCE
2 
+#'
3 
+#' It produces one sample in the result for each sample of the left operand,
4 
+#' by keeping the same metadata of the left input sample and only those regions
5 
+#' (with their schema and values) of the left input sample which do not intersect with any region
6 
+#' in the right operand sample.
7 
+#' The optional \emph{joinby} clause is used to extract a subset of couples
8 
+#' from the cartesian product of two dataset \emph{left_input_data} x \emph{right_input_data}
9 
+#' on which to apply the DIFFERENCE operator:
10 
+#' only those samples that have the same value for each attribute
11 
+#' are considered when performing the difference.
12 
+#'
13 
+#' @importFrom rJava J
14 
+#' @importFrom rJava .jnull
15 
+#' @importFrom rJava .jarray
16 
+#'
17 
+#' @param right_input_data returned object from any GMQL function
18 
+#' @param left_input_data returned object from any GMQL function
19 
+#' @param joinBy list of CONDITION objects, or simple string concatenation
20 
+#' (i.e c("cell_type","attribute_tag","size")).
21 
+#' Every object contains the name of metadata to be used in \emph{groupby}.
22 
+#' For details of CONDITION objects see:
23 
+#' \code{\link{DEF}}, \code{\link{FULL}}, \code{\link{EXACT}}
24 
+#'
25 
+#' Every condition accepts only one string value (e.g. DEF("cell_type") )
26 
+#' In case of single concatenation with no CONDITION, all metadata are considering as DEF
27 
+#'
28 
+#' @param is_exact single logical value: TRUE means that the region difference is executed only
29 
+#' on regions in left_input_data with exactly the same coordinates of at least one region present
30 
+#' in right_input_data; if is_exact = FALSE, the difference is executed on all regions in
31 
+#' left_input_data that overlap with at least one region in right_input_data (even just one base).
32 
+#'
33 
+#' @return DAGgraph class object. It contains the value associated to the graph used
34 
+#' as input for the subsequent GMQL function
35 
+#'
36 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
37 
+#'
38 
+#' @examples
39 
+#'
40 
+#' ## This GMQL statement returns all the regions in the first dataset that do not
41 
+#' ## overlap any region in the second dataset.
42 
+#'
43 
+#' initGMQL("gtf")
44 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
45 
+#' test_path2 <- system.file("example","DATA_SET_VAR_GDM",package = "RGMQL")
46 
+#' r_left = readDataset(test_path)
47 
+#' r_right = readDataset(test_path2)
48 
+#' out = difference(r_left,r_right)
49 
+#'
50 
+#' \dontrun{
51 
+#' ## This GMQL statement extracts for every pair of samples s1 in EXP1 and s2 in EXP2
52 
+#' ## having the same value of the metadata attribute 'antibody_target'
53 
+#' ## the regions that appear in s1 but do not overlap any region in s2;
54 
+#' ## metadata of the result are the same as the metadata of s1.
55 
+#'
56 
+#' initGMQL("gtf")
57 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
58 
+#' test_path2 <- system.file("example","DATA_SET_VAR_GDM",package = "RGMQL")
59 
+#' exp1 = readDataset(test_path)
60 
+#' exp2 = readDataset(test_path2)
61 
+#' out = difference(exp1,exp2, c("antibody_target"))
62 
+#'
63 
+#' }
64 
+#'
65 
+#' @export
66 
+#'
67 
+difference <- function(left_input_data, right_input_data, joinBy = NULL,is_exact = FALSE)
68 
+{
69 
+  if(!is.null(joinBy))
70 
+    join_condition_matrix <- .jarray(.join_condition(joinBy),dispatch = TRUE)
71 
+  else
72 
+    join_condition_matrix <- .jnull("java/lang/String")
73 
+
74 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
75 
+  response <- WrappeR$difference(join_condition_matrix,right_input_data$value,left_input_data$value,is_exact)
76 
+  error <- strtoi(response[1])
77 
+  data <- response[2]
78 
+  if(error!=0)
79 
+    stop(data)
80 
+  else
81 
+    DAGgraph(data)
82 
+}
83 
+
R/Extend.R
History View file @ 43d9e4a
... ... 
@@ -6,6 +6,7 @@
6 6 
 #'
7 7 
 #' @importFrom rJava .jnull
8 8 
 #' @importFrom rJava J
9 
+#' @importFrom rJava .jarray
9 10 
 #'
10 11 
 #' @param input_data returned object from any GMQL function
11 12 
 #' @param metadata list of element in the form \emph{key} = \emph{function_aggregate}.
... ... 
@@ -49,7 +50,7 @@
49 50 
 #' ##  2. MinP is the minimum pvalue of the sample regions.
50 51 
 #' ## res sample regions are the same as the ones in exp.
51 52 
 #'
52 
-#' res = extend(input_data = exp, list(RegionCount = COUNT(),MinP = MIN(pvalue)))
53 
+#' res = extend(input_data = exp, list(RegionCount = COUNT(),MinP = MIN("pvalue")))
53 54 
 #'
54 55 
 #' }
55 56 
 #'
... ... 
@@ -58,7 +59,7 @@
58 59 
 extend <-function(input_data, metadata = NULL)
59 60 
 {
60 61 
   if(!is.null(metadata))
61 
-    metadata_matrix <- .aggregates(metadata,"META_OPERATOR")
62 
+    metadata_matrix <- .jarray(.aggregates(metadata,"META_OPERATOR"),dispatch = TRUE)
62 63 
   else
63 64 
     metadata_matrix <- .jnull("java/lang/String")
64 65
R/Join.R
History View file @ 43d9e4a
65 66 
new file mode 100644
... ... 
@@ -0,0 +1,124 @@
1 
+#' GMQL Operation: JOIN
2 
+#'
3 
+#' It takes in input two datasets, respectively known as nchor (left) and experiment (right) and returns
4 
+#' a dataset of samples consisting of regions extracted from the operands according to the specified condition
5 
+#' (a.k.a genometric_predicate).
6 
+#' The number of generated output samples is the Cartesian product of the number of samples
7 
+#' in the anchor and in the experiment dataset (if joinBy is not specified).
8 
+#' The output metadata are the union of the input metadata, with their attribute names prefixed with
9 
+#' left or right respectively.
10 
+#'
11 
+#' @importFrom rJava .jnull
12 
+#' @importFrom rJava J
13 
+#' @importFrom rJava .jarray
14 
+#'
15 
+#' @param left_input_data returned object from any GMQL function
16 
+#' @param right_input_data returned object from any GMQL function
17 
+#' @param genometric_predicate is a list of lists of DISTAL object by means of logical ANDs
18 
+#' For details of DISTAL objects see:
19 
+#' \code{\link{DLE}}, \code{\link{DGE}}, \code{\link{MD}}, \code{\link{UP}},
20 
+#' \code{\link{DOWN}}, \code{\link{DL}}, \code{\link{DG}}
21 
+#'
22 
+#' @param joinBy list of CONDITION objects, or simple string concatenation
23 
+#' (i.e c("cell_type","attribute_tag","size")).
24 
+#' Every object contains the name of metadata to be used in \emph{groupby}.
25 
+#' For details of CONDITION objects see:
26 
+#' \code{\link{DEF}}, \code{\link{FULL}}, \code{\link{EXACT}}
27 
+#'
28 
+#' Every condition accepts only one string value. (e.g. DEF("cell_type") )
29 
+#' In case of single concatenation with no CONDITION, all metadata are considering as DEF
30 
+#'
31 
+#' @param region_output single string that declare which region is given in output for each input pair of left dataset
32 
+#' right dataset regions satisfying the genometric predicate:
33 
+#' \itemize{
34 
+#' \item{left: outputs the anchor regions from left_input_data that satisfy the genometric predicate}
35 
+#' \item{right: outputs the experiment regions from right_input_data that satisfy the genometric predicate}
36 
+#' \item{int (intersection): outputs the overlapping part (intersection) of the left_input_data and right_input_data
37 
+#' regions that satisfy the genometric predicate; if the intersection is empty, no output is produced}
38 
+#' \item{contig: outputs the concatenation between the left_input_data and right_input_data regions that satisfy
39 
+#' the genometric predicate, (i.e. the output regionis defined as having left (right) coordinates
40 
+#' equal to the minimum (maximum) of the corresponding coordinate values in the left_input_data and right_input_data
41 
+#' regions satisfying the genometric predicate)}
42 
+#' }
43 
+#'
44 
+#' @return DAGgraph class object. It contains the value associated to the graph used
45 
+#' as input for the subsequent GMQL function
46 
+#'
47 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
48 
+#'
49 
+#'
50 
+#' @examples
51 
+#'
52 
+#' ## Given a dataset 'hm' and one called 'tss' with a sample including Transcription Start Site annotations,
53 
+#' ## it searches for those regions of hm that are at a minimal distance from a transcription start site (TSS)
54 
+#' ## and takes the first/closest one for each TSS,
55 
+#' ## provided that such distance is lesser than 120K bases and joined 'tss' and 'hm' samples are obtained
56 
+#' ## from the same provider (joinby clause).
57 
+#'
58 
+#' initGMQL("gtf")
59 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
60 
+#' test_path2 <- system.file("example","DATA_SET_VAR_GDM",package = "RGMQL")
61 
+#' TSS = readDataset(test_path)
62 
+#' HM = readDataset(test_path2)
63 
+#' join_data = join(TSS,HM,genometric_predicate=list(list(MD(1),DLE(120000))),c("provider"),region_output="RIGHT")
64 
+#'
65 
+#' @export
66 
+#'
67 
+join <- function(right_input_data, left_input_data, genometric_predicate = NULL,
68 
+                 joinBy = NULL, region_output="contig")
69 
+{
70 
+
71 
+  if(!is.null(genometric_predicate))
72 
+  {
73 
+    if(!is.list(genometric_predicate))
74 
+      stop("genometric_predicate must be list of lists")
75 
+
76 
+    if(!all(sapply(genometric_predicate, function(x) is.list(x) )))
77 
+      stop("genometric_predicate must be list of lists")
78 
+
79 
+    lapply(genometric_predicate, function(list_pred) {
80 
+      if(length(list_pred)>4)
81 
+      {
82 
+        warning("only 4 element per list, we cut the rest")
83 
+        length(list_pred)=4
84 
+      }
85 
+
86 
+      if(!all(sapply(list_pred, function(x) {is(x,"DISTAL")} )))
87 
+        stop("All elements should be DISTAL object")
88 
+
89 
+    })
90 
+
91 
+    genomatrix <- t(sapply(genometric_predicate, function(list_pred) {
92 
+      dist_array <- sapply(list_pred, function(x) {
93 
+        new_value = as.character(x)
94 
+        array <- c(new_value)
95 
+      })
96 
+      dist_array = c(dist_array,c("NA","NA"),c("NA","NA"),c("NA","NA"))
97 
+      length(dist_array) = 8
98 
+      dist_array
99 
+    }))
100 
+
101 
+    genomatrix <- .jarray(genomatrix, dispatch = TRUE)
102 
+  }
103 
+  else
104 
+    genomatrix <- .jnull("java/lang/String")
105 
+
106 
+  if(!is.null(joinBy))
107 
+    join_condition_matrix <- .jarray(.join_condition(joinBy),dispatch = TRUE)
108 
+  else
109 
+    join_condition_matrix <- .jnull("java/lang/String")
110 
+
111 
+  ouput <- toupper(region_output)
112 
+  if(!identical(ouput,"CONTIG") && !identical(ouput,"LEFT") && !identical(ouput,"RIGHT")
113 
+     && !identical(ouput,"INT"))
114 
+    stop("region_output must be contig,left,right or int (intersection)")
115 
+
116 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
117 
+  response <- WrappeR$join(genomatrix,join_condition_matrix, ouput,right_input_data$value, left_input_data$value)
118 
+  error <- strtoi(response[1])
119 
+  data <- response[2]
120 
+  if(error!=0)
121 
+    stop(data)
122 
+  else
123 
+    DAGgraph(data)
124 
+}
R/Map.R
History View file @ 43d9e4a
0 125 
new file mode 100644
... ... 
@@ -0,0 +1,88 @@
1 
+#' GMQL Operation: MAP
2 
+#'
3 
+#' It computes, for each sample in the right dataset, aggregates over the values of the right regions
4 
+#' that intersect with a region in a left sample, for each region of each sample in the left dataset;
5 
+#' The number of generated output samples is the Cartesian product of the samples in the two input datasets;
6 
+#' each output sample has the same regions as the related input left sample, with their attributes and values,
7 
+#' plus the attributes computed as aggregates over right region values.
8 
+#' Output sample metadata are the union of the related input sample metadata,
9 
+#' whose attribute names are prefixed with "left" or "right" respectively.
10 
+#'
11 
+#' When the joinby clause is present, only pairs of samples of left_input_data and of right_input_data with
12 
+#' metadata M1 and M2 respectively that satisfy the joinby condition are considered.
13 
+#'
14 
+#' The clause consists of a list of metadata attribute names that must be present with equal values
15 
+#' in both M1 and  M2
16 
+#'
17 
+#'
18 
+#' @param left_input_data returned object from any GMQL function
19 
+#' @param right_input_data returned object from any GMQL function
20 
+#' @param aggregates list of element in the form \emph{key} = \emph{function_aggregate}.
21 
+#' The \emph{function_aggregate} is an object of class OPERATOR
22 
+#' The aggregate functions available are: \code{\link{MIN}}, \code{\link{MAX}},
23 
+#' \code{\link{SUM}}, \code{\link{BAG}}, \code{\link{AVG}}, \code{\link{COUNT}},
24 
+#' \code{\link{STD}}, \code{\link{MEDIAN}}, \code{\link{Q1}}, \code{\link{Q2}}, \code{\link{Q3}}.
25 
+#' Every operator accepts a string value, execet for COUNT that cannot have a value.
26 
+#' Argument of 'function_aggregate' must exist in schema
27 
+#' Two style are allowed:
28 
+#' \itemize{
29 
+#' \item list of key-value pairs: e.g. sum = SUM("pvalue")
30 
+#' \item list of values: e.g. SUM("pvalue")
31 
+#' }
32 
+#' "mixed style" is not allowed
33 
+#'
34 
+#' @param joinBy list of CONDITION objects, or simple string concatenation
35 
+#' (i.e c("cell_type","attribute_tag","size")).
36 
+#' Every object contains the name of metadata to be used in \emph{groupby}.
37 
+#' For details of CONDITION objects see:
38 
+#' \code{\link{DEF}}, \code{\link{FULL}}, \code{\link{EXACT}}
39 
+#'
40 
+#' Every condition accepts only one string value. (e.g. DEF("cell_type") )
41 
+#' In case of single concatenation with no CONDITION, all metadata are considering as DEF
42 
+#'
43 
+#' @return DAGgraph class object. It contains the value associated to the graph used
44 
+#' as input for the subsequent GMQL function
45 
+#'
46 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
47 
+#'
48 
+#' @examples
49 
+#'
50 
+#' ## it counts the number of regions in each sample from exp that overlap with a ref region,
51 
+#' ## and for each ref region it computes the minimum score of all the regions in each exp sample
52 
+#' ## that overlap with it.
53 
+#' ## The MAP joinby option ensures that only the exp samples referring to the same 'cell_tissue'
54 
+#' ## of a ref sample are mapped on such ref sample;
55 
+#' ## exp samples with no cell_tissue metadata attribute, or with such metadata
56 
+#' ## but with a different value from the one(s) of ref sample(s), are disregarded.
57 
+#'
58 
+#' initGMQL("gtf")
59 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
60 
+#' test_path2 <- system.file("example","DATA_SET_VAR_GDM",package = "RGMQL")
61 
+#' exp = readDataset(test_path)
62 
+#' ref = readDataset(test_path2)
63 
+#' out = map(ref,exp, list(minScore = MIN("score")), joinBy = c("cell_tissue") )
64 
+#'
65 
+#'
66 
+#' @export
67 
+#'
68 
+map <- function(left_input_data, right_input_data, aggregates = NULL, joinBy = NULL)
69 
+{
70 
+  if(!is.null(aggregates))
71 
+    metadata_matrix <- .jarray(.aggregates(aggregates,"OPERATOR"),dispatch = TRUE)
72 
+  else
73 
+    metadata_matrix = .jnull("java/lang/String")
74 
+
75 
+  if(!is.null(joinBy))
76 
+    join_condition_matrix <- .jarray(.join_condition(joinBy),dispatch = TRUE)
77 
+  else
78 
+    join_condition_matrix <- .jnull("java/lang/String")
79 
+
80 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
81 
+  response<-WrappeR$map(join_condition_matrix,metadata_matrix,left_input_data$value,right_input_data$value)
82 
+  error <- strtoi(response[1])
83 
+  data <- response[2]
84 
+  if(error!=0)
85 
+    stop(data)
86 
+  else
87 
+    DAGgraph(data)
88 
+}
R/Materialize.R
History View file @ 43d9e4a
0 89 
new file mode 100644
... ... 
@@ -0,0 +1,197 @@
1 
+#' GMQL Function: EXECUTE
2 
+#'
3 
+#' execute GMQL query.
4 
+#' The function works only after invoking at least one materialize
5 
+#'
6 
+#' @details
7 
+#'
8 
+#' After invoking execution function, all varialbe associated to DAG will be removed
9 
+#' from scala enviroment, although the associated R variable will remain stored in R environment
10 
+#'
11 
+#' @importFrom rJava J
12 
+#'
13 
+#' @return None
14 
+#'
15 
+#' @examples
16 
+#'
17 
+#' initGMQL()
18 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
19 
+#' r = readDataset(test_path)
20 
+#' s = select(input_data = r)
21 
+#' m = merge(groupBy = c("antibody_targer","cell_karyotype"),input_data = s)
22 
+#' materialize(input_data = m, dir_out = test_path)
23 
+#'
24 
+#' \dontrun{
25 
+#' execute()
26 
+#' }
27 
+#' @export
28 
+#'
29 
+execute <- function()
30 
+{
31 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
32 
+  remote_proc <- WrappeR$is_remote_processing()
33 
+  if(!remote_proc)
34 
+    .download_or_upload()
35 
+
36 
+  response <- WrappeR$execute()
37 
+  error <- strtoi(response[1])
38 
+  data <- response[2]
39 
+  if(error!=0)
40 
+    stop(data)
41 
+  else
42 
+  {
43 
+    if(remote_proc)
44 
+    {
45 
+      url <- WrappeR$get_url()
46 
+      .download_or_upload()
47 
+      serializeQuery(url,FALSE,data)
48 
+    }
49 
+  }
50 
+}
51 
+
52 
+.download_or_upload <- function()
53 
+{
54 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
55 
+  data <- WrappeR$get_dataset_list()
56 
+  data_list <- apply(data, 1, as.list)
57 
+  url <- WrappeR$get_url()
58 
+  remote <- WrappeR$is_remote_processing()
59 
+  if(remote)
60 
+  {
61 
+    sapply(data_list,function(x){
62 
+      uploadSamples(url,x[[2]],x[[1]],x[[3]],FALSE)
63 
+    })
64 
+  }
65 
+  else
66 
+  {
67 
+    sapply(data_list,function(x){
68 
+      downloadDataset(url,x[[2]],x[[1]])
69 
+    })
70 
+  }
71 
+}
72 
+
73 
+#' GMQL Operation: MATERIALIZE
74 
+#'
75 
+#' It saves the contents of a dataset that contains samples metadata and samples regions.
76 
+#' It is normally used to persist the contents of any dataset generated during a GMQL query.
77 
+#' Any dataset can be materialized, but the operation can be very time-consuming.
78 
+#' For best performance, materialize the relevant data only.
79 
+#'
80 
+#' @importFrom rJava J
81 
+#'
82 
+#' @param input_data returned object from any GMQL function
83 
+#' @param dir_out destination folder path.
84 
+#' by default is current working directory of the R process
85 
+#'
86 
+#' @return None
87 
+#'
88 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
89 
+#'
90 
+#' @examples
91 
+#'
92 
+#' initGMQL("gtf")
93 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
94 
+#' r = readDataset(test_path)
95 
+#' s = select(input_data = r)
96 
+#' m = merge(groupBy = c("antibody_targer","cell_karyotype"),input_data = s)
97 
+#' materialize(input_data = m, dir_out = test_path)
98 
+#'
99 
+#' @export
100 
+#'
101 
+materialize <- function(input_data, dir_out = getwd())
102 
+{
103 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
104 
+  response <- WrappeR$materialize(input_data$value,dir_out)
105 
+  error <- strtoi(response[1])
106 
+  data <- response[2]
107 
+  if(error!=0)
108 
+    stop(data)
109 
+  else
110 
+    invisible(NULL)
111 
+}
112 
+
113 
+
114 
+#' GMQL Operation: TAKE
115 
+#'
116 
+#' It saves the contents of a dataset that contains samples metadata and samples regions.
117 
+#' It is normally used to store in memoery the contents of any dataset generated during a GMQL query.
118 
+#' the operation can be very time-consuming.
119 
+#' If you have invoked any materialization before take function, all those dataset will be materialized
120 
+#' as folder (like if execution was invoked)
121 
+#'
122 
+#' @import GenomicRanges
123 
+#' @importFrom stats setNames
124 
+#' @importFrom rJava J
125 
+#' @importFrom rJava .jevalArray
126 
+#'
127 
+#' @param input_data returned object from any GMQL function
128 
+#' @param rows number of rows for each sample regions that you want to retrieve and stored in memory
129 
+#' by default is 0 that means take all rows for each sample
130 
+#'
131 
+#' @return GrangesList with associated metadata
132 
+#'
133 
+#' @examples
134 
+#'
135 
+#' initGMQL()
136 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
137 
+#' r = readDataset(test_path)
138 
+#' m = merge(groupBy = c("antibody_target","cell_karyotype"),input_data = r)
139 
+#' g <- take(input_data = m, rows = 45)
140 
+#'
141 
+#' @export
142 
+#'
143 
+take <- function(input_data, rows=0L)
144 
+{
145 
+  rows <- as.integer(rows[1])
146 
+  if(rows<0)
147 
+    stop("rows cannot be negative")
148 
+
149 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
150 
+  response <- WrappeR$take(input_data$value,rows)
151 
+  error <- strtoi(response[1])
152 
+  data <- response[2]
153 
+  if(error!=0)
154 
+    stop(data)
155 
+
156 
+  reg <- .jevalArray(WrappeR$get_reg(),simplify = TRUE)
157 
+  if(is.null(reg))
158 
+    stop("no regions defined")
159 
+  meta <- .jevalArray(WrappeR$get_meta(),simplify = TRUE)
160 
+  if(is.null(meta))
161 
+    stop("no metadata defined")
162 
+  schema <- .jevalArray(WrappeR$get_schema(),simplify = TRUE)
163 
+  if(is.null(schema))
164 
+    stop("no schema defined")
165 
+
166 
+  reg_data_frame <- as.data.frame(reg)
167 
+  list <- split(reg_data_frame, reg_data_frame[1])
168 
+  names <- c("seqname","start","end","strand",schema)
169 
+
170 
+  sampleList <- lapply(list, function(x){
171 
+    x <- x[-1]
172 
+    names(x) <- names
173 
+    g <- GenomicRanges::makeGRangesFromDataFrame(x,keep.extra.columns = TRUE,
174 
+                                                 start.field = "start",end.field = "end")
175 
+  })
176 
+  gRange_list <- GRangesList(sampleList)
177 
+
178 
+  meta_list <- .metadata_from_frame_to_list(meta)
179 
+
180 
+  S4Vectors::metadata(gRange_list) <- meta_list
181 
+  return(gRange_list)
182 
+}
183 
+
184 
+.metadata_from_frame_to_list <- function(metadata_frame)
185 
+{
186 
+  meta_frame <- as.data.frame(metadata_frame)
187 
+  list <- split(meta_frame, meta_frame[1])
188 
+  name_value_list <- lapply(list, function(x){
189 
+    x <- x[-1]
190 
+  })
191 
+  meta_list <- lapply(name_value_list, function(x){
192 
+    stats::setNames(as.list(as.character(x[[2]])), x[[1]])
193 
+  })
194 
+}
195 
+
196 
+
197 
+
R/Merge.R
History View file @ 43d9e4a
0 198 
new file mode 100644
... ... 
@@ -0,0 +1,60 @@
1 
+#' GMQL Operation: MERGE
2 
+#'
3 
+#' It builds a dataset consisting of a single sample having as many regions
4 
+#' as the numebr of regions of the input data and as many metadata as the union of
5 
+#' the 'attribute-value' tuples of the input samples.
6 
+#' A groupby clause can be specified on metadata: the samples are then partitioned in groups,
7 
+#' each with a distinct value of the grouping metadata attributes.
8 
+#' The operation is separately applied to each group, yielding one sample in the result for each group.
9 
+#' Samples whose names are not present in the grouping metadata parameter are disregarded.
10 
+#'
11 
+#' @importFrom rJava J
12 
+#' @importFrom rJava .jnull
13 
+#' @importFrom rJava .jarray
14 
+#'
15 
+#' @param input_data returned object from any GMQL function
16 
+#' @param groupBy list of CONDITION objects, or simple string concatenation
17 
+#' (i.e c("cell_type","attribute_tag","size")).
18 
+#' Every object contains the name of metadata to be used in \emph{groupBy}.
19 
+#' For details of CONDITION objects see:
20 
+#' \code{\link{DEF}}, \code{\link{FULL}}, \code{\link{EXACT}}
21 
+#'
22 
+#' Every condition accepts only one string value (e.g. DEF("cell_type") )
23 
+#' In case of single concatenation with no CONDITION, all metadata are considering as DEF
24 
+#'
25 
+#' @return DAGgraph class object. It contains the value associated to the graph used
26 
+#' as input for the subsequent GMQL function
27 
+#'
28 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
29 
+#'
30 
+#' @examples
31 
+#'
32 
+#' ## it creates a dataset called merged which contains one sample for each antibody_target value
33 
+#' ## found within the metadata of the exp dataset sample;
34 
+#' ## each created sample contains all regions from all 'exp' samples with a specific value for their
35 
+#' ## antibody_target metadata attribute.
36 
+#'
37 
+#' initGMQL("gtf")
38 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
39 
+#' exp = readDataset(test_path)
40 
+#' merged = merge(input_data = exp, groupBy = c("antibody_target"))
41 
+#'
42 
+#' @export
43 
+#'
44 
+merge <- function(input_data, groupBy = NULL)
45 
+{
46 
+  if(!is.null(groupBy))
47 
+    join_condition_matrix <- .jarray(.join_condition(groupBy),dispatch = TRUE)
48 
+  else
49 
+    join_condition_matrix <- .jnull("java/lang/String")
50 
+
51 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
52 
+  response <- WrappeR$merge(join_condition_matrix,input_data$value)
53 
+  error <- strtoi(response[1])
54 
+  data <- response[2]
55 
+  if(error!=0)
56 
+    stop(data)
57 
+  else
58 
+    DAGgraph(data)
59 
+}
60 
+
R/Order.R
History View file @ 43d9e4a
0 61 
new file mode 100644
... ... 
@@ -0,0 +1,166 @@
1 
+#' GMQL operation: ORDER
2 
+#'
3 
+#' It is used to order either samples or sample regions or both,
4 
+#' according to a set of metadata and/or region attributes, and/or region coordinates.
5 
+#' Order can be specified as ascending / descending for every attribute
6 
+#' The number of samples and their regions remain the same (unless mtop/rtop parameters specified)
7 
+#' but a new ordering metadata and/or region attribute is added.
8 
+#' Sorted samples or regions have a new attribute "order", added to either metadata, or regions,
9 
+#' or both of them as specified in input
10 
+#' The input mtop = k and rtop = m extracts the first k samples and m regions respectively,
11 
+#' the clause mtopg = k and rtopg = m performs grouping operation,
12 
+#' grouping by identical values of ordering attributes
13 
+#' and then selects the first k samples or regions of each group
14 
+#'
15 
+#' @importFrom rJava J
16 
+#' @importFrom rJava .jnull
17 
+#' @importFrom rJava .jarray
18 
+#'
19 
+#' @param input_data "url-like" string taken from GMQL function
20 
+#' @param metadata_ordering list of ORDER objects where every object contains the name of metadata
21 
+#' The ORDER's available are: \code{\link{ASC}}, \code{\link{DESC}}
22 
+#' Every condition accepts only one string value. (e.g. ASC("cell_type") )
23 
+#' @param mtop integer value specifying the first k samples.
24 
+#' default is 0 that means every sample must be considered
25 
+#' @param mtopg integer value specifying the first j samples in each group.
26 
+#' default is 0 that means every sample must be considered
27 
+#' @param mtopp integer value specifying the first j samples in each group.
28 
+#' default is 0 that means every sample must be considered
29 
+#' @param regions_ordering list of ORDER objects where every object contains the name of region schema value
30 
+#' The ORDER's available are: ASC, DESC.
31 
+#' Every condition accepts only one string value. (e.g. DESC("pvalue") )
32 
+#' @param rtop integer value specifying the first m samples in each group.
33 
+#' default is 0 that means every sample must be considered
34 
+#' @param rtopg integer value specifying the first i samples in each group.
35 
+#' default is 0 that means every sample must be considered
36 
+#' @param rtopp integer value specifying the first i samples in each group.
37 
+#' default is 0 that means every sample must be considered
38 
+#'
39 
+#'
40 
+#' @return DAGgraph class object. It contains the value associated to the graph used
41 
+#' as input for the subsequent GMQL function
42 
+#'
43 
+#' @details
44 
+#' mtop, mtopg,mtopp, rtop, rtopg and rtopp are normally numbers: if you specify a vector,
45 
+#' only the first element will be used
46 
+#' mtop and mtopg and mtopp are mutalbe exclusive, so rtop and rtopg and rtopp
47 
+#'
48 
+#'
49 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
50 
+#'
51 
+#' @examples
52 
+#'
53 
+#' ## it orders the samples according to the Region_count metadata attribute and takes the two samples
54 
+#' ## that have the highest count.
55 
+#'
56 
+#' initGMQL("gtf")
57 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
58 
+#' r = readDataset(test_path)
59 
+#' o = order(r,list(DESC("Region_Count")), mtop = 2)
60 
+#'
61 
+#' @export
62 
+#'
63 
+order <- function(input_data, metadata_ordering = NULL, mtop = 0, mtopg = 0,mtopp = 0,
64 
+                  regions_ordering = NULL,rtop = 0,rtopg = 0,rtopp = 0)
65 
+{
66 
+  if(!is.numeric(mtop) || !is.numeric(mtopg) || !is.numeric(rtop) || !is.numeric(rtopg)
67 
+     || !is.numeric(mtopp)|| !is.numeric(rtopp))
68 
+    stop("mtop, rtop, rtopg and mtopg must be integer")
69 
+
70 
+  if(length(mtop)>0 || length(mtopg)>0 || length(rtop)>0 || length(rtopg)>0
71 
+     || length(mtopp)>0 || length(rtopp)>0)
72 
+    warning("only the first element is taken by rtop, mtop, mtopg, rtopg, rtopp, mtopp")
73 
+
74 
+  # we consider only the first element even if input is a vector of Int
75 
+  # we cut the other arguments
76 
+
77 
+  mtop = as.integer(mtop[1])
78 
+  mtopg = as.integer(mtopg[1])
79 
+  mtopp = as.integer(mtopp[1])
80 
+
81 
+  rtop = as.integer(rtop[1])
82 
+  rtopg = as.integer(rtopg[1])
83 
+  rtopp = as.integer(rtopp[1])
84 
+
85 
+  if(mtop > 0 && mtopg >0)
86 
+  {
87 
+    warning("cannot be used together.\nWe set mtopg = 0")
88 
+    mtopg = 0L
89 
+  }
90 
+
91 
+  if(mtop >0 && mtopp>0)
92 
+  {
93 
+    warning("cannot be used together.\nWe set mtopp = 0")
94 
+    mtopp = 0L
95 
+  }
96 
+
97 
+  if(mtopg >0 && mtopp>0)
98 
+  {
99 
+    warning("cannot be used together.\nWe set mtopp = 0")
100 
+    mtopp = 0L
101 
+  }
102 
+
103 
+  if(rtop > 0 && rtopg >0)
104 
+  {
105 
+    warning("cannot be used together.\nWe set rtopg = 0")
106 
+    rtopg = 0L
107 
+  }
108 
+
109 
+  if(rtop >0 && rtopp>0)
110 
+  {
111 
+    warning("cannot be used together.\nWe set rtopp = 0")
112 
+    rtopp = 0L
113 
+  }
114 
+
115 
+  if(rtopg >0 && rtopp>0)
116 
+  {
117 
+    warning("cannot be used together.\nWe set rtopp = 0")
118 
+    rtopp = 0L
119 
+  }
120 
+
121 
+  if(!is.null(metadata_ordering))
122 
+    meta_matrix <- .jarray(.ordering_meta(metadata_ordering),dispatch = TRUE)
123 
+  else
124 
+    meta_matrix <- .jnull("java/lang/String")
125 
+
126 
+  if(!is.null(regions_ordering))
127 
+    region_matrix <- .jarray(.ordering_meta(regions_ordering),dispatch = TRUE)
128 
+  else
129 
+    region_matrix <- .jnull("java/lang/String")
130 
+
131 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
132 
+  response <- WrappeR$order(meta_matrix,mtopg,mtop,mtopp,region_matrix,rtopg,rtop,rtopp,input_data$value)
133 
+  error <- strtoi(response[1])
134 
+  data <- response[2]
135 
+  if(error!=0)
136 
+    stop(data)
137 
+  else
138 
+    DAGgraph(data)
139 
+}
140 
+
141 
+
142 
+.ordering_meta <- function(ordering)
143 
+{
144 
+  if(is.list(ordering))
145 
+  {
146 
+    order_matrix <- t(sapply(ordering,function(x){
147 
+      new_value <- as.character(x)
148 
+      if(length(new_value)==1)
149 
+        new_value = c("ASC",new_value)
150 
+      else if(!identical("ASC",new_value[1]) && !identical("DESC",new_value[1]))
151 
+        stop("no more than one value")
152 
+      matrix <- matrix(new_value)
153 
+    }))
154 
+  }
155 
+  else if(is.character(ordering))
156 
+  {
157 
+    order_matrix <- t(sapply(ordering, function(x) {
158 
+      new_value = c("ASC",x)
159 
+      matrix <- matrix(new_value)
160 
+    }))
161 
+  }
162 
+  else
163 
+    stop("only list or character")
164 
+}
165 
+
166 
+
R/Project.R
History View file @ 43d9e4a
0 167 
new file mode 100644
... ... 
@@ -0,0 +1,132 @@
1 
+#' GMQL Operation: PROJECT
2 
+#'
3 
+#' It creates, from an existing dataset, a new dataset with all the samples from input dataset
4 
+#' but keeping for each sample in the input dataset only those metadata and/or region attributes
5 
+#' expressed in the operator parameter list.
6 
+#' Region coordinates and values of the remaining metadata remain equal to those in the input dataset.
7 
+#' It allows to:
8 
+#' \itemize{
9 
+#' \item{Remove existing metadata and/or region attributes from a dataset}
10 
+#' \item{Create new metadata and/or region attributes in the result}
11 
+#' }
12 
+#'
13 
+#' @importFrom rJava J
14 
+#' @importFrom rJava .jnull
15 
+#' @importFrom rJava .jarray
16 
+#'
17 
+#' @param input_data string pointer taken from GMQL function
18 
+#' @param metadata vector of string made up by metadata attribute
19 
+#' @param regions vector of string made up by schema field attribute
20 
+#' @param all_but_reg logical value indicating which schema filed attribute you want to exclude.
21 
+#' If FALSE only the regions you choose is kept in the output of the project operation,
22 
+#' if TRUE the schema region are all except ones include in region parameter.
23 
+#' if regions is not defined \emph{all_but_reg} is not considerd.
24 
+#' @param all_but_meta logical value indicating which metadata you want to exclude.
25 
+#' If FALSE only the metadata you choose is kept in the output of the project operation,
26 
+#' if TRUE the metadata are all except ones include in region parameter.
27 
+#' if metadata is not defined \emph{all_but_meta} is not considerd.
28 
+#' @param regions_update single string predicate made up by operation on schema field attribute
29 
+#' @param metadata_update single string predicate made up by operation on metadata attribute
30 
+#'
31 
+#' @return DAGgraph class object. It contains the value associated to the graph used
32 
+#' as input for the subsequent GMQL function#'
33 
+#'
34 
+#' @references \url{http://www.bioinformatics.deib.polimi.it/genomic_computing/GMQL/doc/GMQLUserTutorial.pdf}
35 
+#'
36 
+#'
37 
+#' @examples
38 
+#'
39 
+#' ## it creates a new dataset called CTCF_NORM_SCORE by preserving all region attributes apart from score,
40 
+#' ## and creating a new region attribute called new_score by dividing the existing score value
41 
+#' ## of each region by 1000.0 and incrementing it by 100.
42 
+#' ## It also generates, for each sample of the new dataset,
43 
+#' ## a new metadata attribute called normalized with value 1, which can be used in future selections.
44 
+#'
45 
+#' initGMQL("gtf")
46 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
47 
+#' input = readDataset(test_path)
48 
+#' CTCF_NORM_SCORE = project(input,metadata_update="normalized AS 1", regions_update="new_score AS (score / 1000.0) + 100" , regions=c("score"), all_but_reg=TRUE)
49 
+#'
50 
+#'
51 
+#' \dontrun{
52 
+#'
53 
+#' ## it produces an output dataset that contains the same samples as the input dataset.
54 
+#' ## Each output sample only contains, as region attributes,
55 
+#' ## the four basic coordinates (chr, left, right, strand) and the specified region attributes
56 
+#' ## 'variant_classification' and 'variant_type', and as metadata attributes only the specified ones,
57 
+#' ## i.e. manually_curated__tissue_status and manually_curated__tumor_tag.
58 
+#'
59 
+#' initGMQL("gtf")
60 
+#' test_path <- system.file("example","DATA_SET_VAR_GTF",package = "RGMQL")
61 
+#' DS_in = readDataset(test_path)
62 
+#' DS_out = project(DS_in,regions=c("variant_classification", "variant_type"),
63 
+#' metadata=c("manually_curated__tissue_status","manually_curated__tumor_tag"))
64 
+#'
65 
+#' }
66 
+#'
67 
+#' @export
68 
+#'
69 
+#'
70 
+project <-function(input_data, metadata = NULL,metadata_update=NULL,all_but_meta = FALSE,
71 
+                   regions = NULL, regions_update = NULL,all_but_reg=FALSE)
72 
+{
73 
+  if(!is.null(metadata))
74 
+  {
75 
+    if(!is.character(metadata))
76 
+      stop("metadata: no valid input")
77 
+
78 
+    metadata <- metadata[!metadata %in% ""]
79 
+    metadata <- metadata[!duplicated(metadata)]
80 
+
81 
+    if(length(metadata)==0)
82 
+      metadata <- .jnull("java/lang/String")
83 
+
84 
+    metadata <- .jarray(metadata)
85 
+  }
86 
+  else
87 
+    metadata <- .jnull("java/lang/String")
88 
+
89 
+  if(!is.null(regions))
90 
+  {
91 
+    if(!is.character(regions))
92 
+      stop("regions: no valid input")
93 
+
94 
+    regions = regions[!regions %in% ""]
95 
+    regions = regions[!duplicated(regions)]
96 
+
97 
+    if(length(regions)==0)
98 
+      regions <- .jnull("java/lang/String")
99 
+
100 
+    regions <- .jarray(regions)
101 
+  }
102 
+  else
103 
+    regions <- .jnull("java/lang/String")
104 
+
105 
+  if(!is.null(regions_update))
106 
+    .check_predicate(regions_update)
107 
+  else
108 
+    regions_update <- .jnull("java/lang/String")
109 
+
110 
+  if(!is.null(metadata_update))
111 
+    .check_predicate(metadata_update)
112 
+  else
113 
+    metadata_update <- .jnull("java/lang/String")
114 
+
115 
+  if(length(all_but_meta)>1)
116 
+    warning("all_but_meta: no multiple values")
117 
+
118 
+  if(length(all_but_reg)>1)
119 
+    warning("all_but_reg: no multiple values")
120 
+  all_but_reg <- all_but_reg[1]
121 
+  all_but_meta <- all_but_meta[1]
122 
+
123 
+  WrappeR <- J("it/polimi/genomics/r/Wrapper")
124 
+  response <- WrappeR$project(metadata,metadata_update,all_but_meta,
125 
+                              regions,regions_update,all_but_reg,input_data$value)
126 
+  error <- strtoi(response[1])
127 
+  data <- response[2]
128 
+  if(error!=0)
129 
+    stop(data)
130 
+  else
131 
+    DAGgraph(data)
132 
+}
R/Read.R
History View file @ 43d9e4a
... ... 
@@ -120,7 +120,7 @@ readDataset <- function(dataset, parser = "CustomParser", is_local=TRUE,
120 120 
   }
121 121 
   else
122 122 
   {
123 
-    url <- Wrapper$get_url()
123 
+    url <- WrappeR$get_url()
124 124 
     if(is.null(url))
125 125 
       stop("You have to log on using login function")
126 126
R/Select.R
History View file @ 43d9e4a
127 127 
new file mode 100644
... ... 
@@ -0,0 +1,120 @@
1 
+#' GMQL Operation: SELECT
2 
+#'
3 
+#' It extracts a subset of samples from the input dataset.
4 
+#' It returns all the samples satisfying the predicate on metadata.
5 
+#' If regions are specified, returns regions satisfying the predicate on regions.
6 
+#' If semijoin clauses are specified they are applied, too.
7 
+#' When semijoin is defined, it extracts those samples containing all metadata attribute defined in semijoin clause
8 
+#' with at least one metadata value in common with semi join dataset