1. RGMQL
  2. Commit 54f1b5c5dd51059c06f183b492b3382af9d5f0c8
Browse code

new vignette

Simone authored on 01/02/2018 20:01:52
Showing 10 changed files
inst/example/DATASET_META/files/S_00000.gdm
History View file @ 54f1b5c
1 1 
new file mode 100755
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1 
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+chr15	74489678	74489764	-	NM_001199041	0
303 
+chr15	74489678	74489764	-	NM_001199040	0
304 
+chr15	74489678	74489764	-	NM_001199042	0
305 
+chr15	74489678	74489764	-	NM_001142617	0
306 
+chr15	74489678	74489764	-	NM_001142618	0
307 
+chr15	74489678	74489764	-	NM_022369	0
308 
+chr15	74490092	74490159	-	NM_001142620	0
309 
+chr15	74490092	74490159	-	NM_001142619	0
310 
+chr15	74490092	74490159	-	NM_001199041	0
311 
+chr15	74490092	74490159	-	NM_001199040	0
312 
+chr15	74490092	74490159	-	NM_001199042	0
313 
+chr15	74490092	74490159	-	NM_001142617	0
314 
+chr15	74490092	74490159	-	NM_001142618	0
315 
+chr15	74490092	74490159	-	NM_022369	0
316 
+chr18	32455202	32455362	+	NM_001198940	0
317 
+chr18	32455202	32455362	+	NM_001390	0
318 
+chr18	32455202	32455362	+	NM_001198942	0
319 
+chr18	32455202	32455362	+	NM_001198944	0
320 
+chr18	32455202	32455362	+	NM_001198943	0
321 
+chr18	32455202	32455362	+	NM_032980	0
322 
+chr18	32457682	32457772	+	NM_001198939	0
323 
+chr18	32457682	32457772	+	NM_001198938	0
324 
+chr18	32457682	32457772	+	NM_032975	0
325 
+chr18	32457682	32457772	+	NM_001198940	0
326 
+chr18	32457682	32457772	+	NM_001390	0
327 
+chr18	32457682	32457772	+	NM_001198942	0
328 
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329 
+chr18	32457682	32457772	+	NM_001198943	0
330 
+chr18	32457682	32457772	+	NM_032980	0
331 
+chr18	32459514	32459683	+	NM_001198939	0
332 
+chr18	32459514	32459683	+	NM_001198938	0
333 
+chr18	32459514	32459683	+	NM_032975	0
334 
+chr18	32459514	32459683	+	NM_001198940	0
335 
+chr18	32459514	32459683	+	NM_001390	0
336 
+chr18	32459514	32459683	+	NM_001198942	0
337 
+chr18	32459514	32459683	+	NM_001198944	0
338 
+chr18	32459514	32459683	+	NM_001198943	0
339 
+chr18	32459514	32459683	+	NM_032980	0
340 
+chr18	32462032	32462165	+	NM_001198939	0
341 
+chr18	32462032	32462165	+	NM_001198938	0
342 
+chr18	32462032	32462165	+	NM_032975	0
343 
+chr18	32462032	32462165	+	NM_001198940	0
344 
+chr18	32462032	32462165	+	NM_001390	0
345 
+chr18	32462032	32462165	+	NM_001198942	0
346 
+chr18	32462032	32462165	+	NM_001198944	0
347 
+chr18	32462032	32462165	+	NM_001198943	0
348 
+chr18	32462032	32462165	+	NM_032980	0
349 
+chr18	32464691	32464740	+	NM_001198939	0
350 
+chr18	32464691	32464740	+	NM_032975	0
351 
+chr18	32464691	32464740	+	NM_001198940	0
352 
+chr18	32464691	32464740	+	NM_001390	0
353 
+chr18	32464691	32464740	+	NM_001198942	0
354 
+chr18	32464691	32464740	+	NM_001198944	0
355 
+chr18	32464691	32464740	+	NM_001198943	0
356 
+chr18	32464691	32464740	+	NM_032980	0
357 
+chr18	32467729	32471808	+	NM_001198939	0
358 
+chr18	32467729	32471808	+	NM_032975	0
359 
+chr18	32467729	32471808	+	NM_001198940	0
360 
+chr18	32467729	32471808	+	NM_001390	0
361 
+chr18	32467729	32471808	+	NM_001198942	0
362 
+chr18	32467729	32471808	+	NM_001198944	0
363 
+chrY	25325643	25325783	-	NM_004081	0
364 
+chrY	25325872	25325936	-	NM_004081	0
365 
+chrY	25326372	25326424	-	NM_004081	0
366 
+chrY	25326984	25327076	-	NM_004081	0
367 
+chrY	25327350	25327497	-	NM_004081	0
368 
+chrY	25336491	25336631	-	NM_004081	0
369 
+chrY	25336491	25336631	-	NM_001005375	0
370 
+chrY	25336720	25336784	-	NM_004081	0
371 
+chrY	25336720	25336784	-	NM_001005375	0
372 
+chrY	25337220	25337272	-	NM_004081	0
373 
+chrY	25337220	25337272	-	NM_001005375	0
374 
+chrY	25337832	25337924	-	NM_004081	0
375 
+chrY	25337832	25337924	-	NM_001005375	0
376 
+chrY	25338198	25338345	-	NM_004081	0
377 
+chrY	25338198	25338345	-	NM_001005375	0
378 
+chrY	25344944	25345239	-	NM_004081	0
379 
+chrY	25344944	25345254	-	NM_020420	0
380 
+chrY	25344944	25345254	-	NM_001005375	0
381 
+chrY	25365580	25365890	+	NM_020364	0
382 
+chrY	25365580	25365890	+	NM_020420	0
383 
+chrY	25365603	25365890	+	NM_020363	0
384 
+chrY	25365603	25365890	+	NM_001005785	0
385 
+chrY	25365603	25365890	+	NM_001005786	0
386 
+chrY	25372490	25372637	+	NM_020363	0
387 
+chrY	25372490	25372637	+	NM_020364	0
388 
+chrY	25372490	25372637	+	NM_001005785	0
389 
+chrY	25372490	25372637	+	NM_020420	0
390 
+chrY	25372490	25372637	+	NM_001005786	0
391 
+chrY	25372911	25373003	+	NM_020363	0
392 
+chrY	25372911	25373003	+	NM_020364	0
393 
+chrY	25372911	25373003	+	NM_001005785	0
394 
+chrY	25372911	25373003	+	NM_020420	0
395 
+chrY	25372911	25373003	+	NM_001005786	0
396 
+chrY	25373563	25373615	+	NM_020363	0
397 
+chrY	25373563	25373615	+	NM_020364	0
398 
+chrY	25373563	25373615	+	NM_001005785	0
399 
+chrY	25373563	25373615	+	NM_020420	0
400 
+chrY	25373563	25373615	+	NM_001005786	0
401 
+chrY	25374051	25374115	+	NM_020363	0
402 
+chrY	25374051	25374115	+	NM_020364	0
403 
+chrY	25374051	25374115	+	NM_001005785	0
404 
+chrY	25374051	25374115	+	NM_020420	0
405 
+chrY	25374051	25374115	+	NM_001005786	0
406 
+chr5	133901805	133902270	+	NM_001289984	0
407 
+chr5	133901805	133902270	+	NM_001289985	0
408 
+chr5	133909334	133909452	+	NM_015288	0
409 
+chr5	133909334	133909452	+	NM_001289984	0
410 
+chr5	133909334	133909452	+	NM_001289985	0
411 
+chr5	133912457	133912586	+	NM_001289985	0
412 
+chr5	133914183	133918920	+	NM_001289984	0
413 
+chr5	133914183	133918920	+	NM_001289985	0
414 
+chr5	133914186	133918920	+	NM_015288	0
415 
+chr5	133936838	133942756	-	NM_001033503	0
416 
+chr5	133936838	133942756	-	NM_016103	0
417 
+chr5	133944061	133944193	-	NM_001033503	0
418 
+chr5	133944061	133944193	-	NM_016103	0
419 
+chr5	133945260	133945364	-	NM_001033503	0
420 
+chr5	133945260	133945364	-	NM_016103	0
421 
+chr5	133948380	133948446	-	NM_001033503	0
422 
+chr5	133948380	133948446	-	NM_016103	0
423 
+chr5	133956622	133956742	-	NM_001033503	0
424 
+chr5	133956622	133956742	-	NM_016103	0
425 
+chr5	133959651	133959727	-	NM_001033503	0
426 
+chr5	133959651	133959727	-	NM_016103	0
427 
+chr5	133967766	133967885	-	NM_001033503	0
428 
+chr5	133968417	133968533	-	NM_001033503	0
429 
+chr5	133968417	133968533	-	NM_016103	0
430 
+chr5	133984474	133984863	+	NM_001252231	0
431 
+chr5	133984474	133984863	+	NM_021982	0
432 
+chr5	133996808	133997276	+	NM_001252231	0
433 
+chr5	133996808	133997276	+	NM_021982	0
434 
+chr5	134002512	134002686	+	NM_001252231	0
435 
+chr5	134002512	134002686	+	NM_021982	0
436 
+chr5	134007498	134007576	+	NM_001252231	0
437 
+chr5	134007498	134007576	+	NM_021982	0
438 
+chr5	134010304	134010465	+	NM_001252231	0
439 
+chr5	134010304	134010465	+	NM_021982	0
440 
+chr5	134010734	134010907	+	NM_001252231	0
441 
+chr5	134010734	134010907	+	NM_021982	0
442 
+chr5	134011712	134011815	+	NM_001252231	0
443 
+chr5	134011712	134011815	+	NM_021982	0
444 
+chr5	134015291	134015418	+	NM_001252231	0
445 
+chr5	134015291	134015418	+	NM_021982	0
446 
+chr5	134018062	134018172	+	NM_001252231	0
447 
+chr5	134018062	134018172	+	NM_021982	0
448 
+chr5	134022479	134022592	+	NM_001252231	0
449 
+chr5	134022479	134022592	+	NM_021982	0
450 
+chr5	134023870	134023989	+	NM_001252231	0
451 
+chr5	134023870	134023989	+	NM_021982	0
452 
+chr5	134028291	134028347	+	NM_001252231	0
453 
+chr5	134028291	134028347	+	NM_021982	0
454 
+chr8	6673378	6673440	-	NM_207411	0
455 
+chr8	6673378	6673440	-	NM_001289973	0
456 
+chr8	6679390	6679560	-	NM_207411	0
457 
+chr8	6679390	6679560	-	NM_001289973	0
458 
+chr8	6681042	6681252	-	NM_207411	0
459 
+chr8	6681042	6681252	-	NM_001289973	0
460 
+chr8	6682686	6682871	-	NM_207411	0
461 
+chr8	6682686	6682871	-	NM_001289973	0
462 
+chr8	6686690	6686828	-	NM_001289973	0
463 
+chr8	6690238	6690422	-	NM_207411	0
464 
+chr8	6690238	6690422	-	NM_001289973	0
465 
+chr8	6692957	6693166	-	NM_207411	0
466 
+chr8	6692957	6693166	-	NM_001289973	0
467 
+chr8	6693075	6693139	+	NR_045217	0
468 
+chr8	6693487	6693743	+	NR_045217	0
469 
+chr8	6699189	6699975	+	NR_045217	0
470 
+chr8	6728096	6728348	-	NM_005218	0
471 
+chr8	6735318	6735529	-	NM_005218	0
472 
+chr8	6782215	6782449	-	NM_001926	0
473 
+chr8	6783364	6783598	-	NM_001926	0
474 
+chr8	6793344	6793663	-	NM_001925	0
475 
+chr8	6794249	6794433	-	NM_001925	0
476 
+chr8	6795747	6795786	-	NM_001925	0
477 
+chr8	6808247	6808360	-	NR_073407	0
478 
+chr8	6808949	6809121	-	NR_073407	0
479 
+chr8	6816810	6816923	-	NR_073408	0
480 
+chr8	6817511	6817683	-	NR_073408	0
481 
+chr8	6825662	6825769	-	NR_029386	0
482 
+chr8	6826451	6826635	-	NR_029386	0
483 
+chr8	6835170	6835401	-	NM_004084	0
484 
+chr8	6835170	6835401	-	NM_001042500	0
485 
+chr8	6835981	6836168	-	NM_004084	0
486 
+chr8	6835981	6836168	-	NM_001042500	0
487 
+chr8	6837534	6837614	-	NM_004084	0
488 
+chr8	6837534	6837614	-	NM_001042500	0
489 
+chr8	6844699	6844945	-	NR_036687	0
490 
+chr8	6844699	6844945	-	NR_036686	0
491 
+chr8	6845621	6845808	-	NR_036687	0
492 
+chr8	6845621	6845808	-	NR_036686	0
493 
+chr8	6847180	6847243	-	NR_036687	0
494 
+chr8	6847180	6847243	-	NR_036686	0
495 
+chr8	6854287	6854518	-	NM_004084	0
496 
+chr8	6854287	6854518	-	NM_001042500	0
497 
+chr8	6855098	6855285	-	NM_004084	0
498 
+chr8	6855098	6855285	-	NM_001042500	0
499 
+chr6_mann_hap4	2998164	2998211	-	NM_001177515	0
500 
+chr6_mann_hap4	2998164	2998211	-	NR_033489	0
501 
+chr6_mann_hap4	2998164	2998211	-	NM_021160	0
502 
+chr6_mann_hap4	2998164	2998211	-	NR_033488	0
503 
+chr6_mann_hap4	2998308	2998407	-	NM_001177515	0
504 
+chr6_mann_hap4	2998308	2998407	-	NR_033489	0
505 
+chr6_mann_hap4	2998308	2998407	-	NM_021160	0
506 
+chr6_mann_hap4	2998308	2998407	-	NR_033488	0
507 
+chr6_mann_hap4	2998490	2998567	-	NM_001177515	0
508 
+chr6_mann_hap4	2998490	2998567	-	NR_033489	0
509 
+chr6_mann_hap4	2998490	2998567	-	NM_021160	0
510 
+chr6_mann_hap4	2998490	2998567	-	NR_033488	0
511 
+chr6_mann_hap4	2998707	2998770	-	NM_001177515	0
512 
+chr6_mann_hap4	2998707	2998770	-	NR_033489	0
513 
+chr6_mann_hap4	2998707	2998770	-	NM_021160	0
514 
+chr6_mann_hap4	2998707	2998770	-	NR_033488	0
515 
+chr6_mann_hap4	2998915	2998972	-	NM_001177515	0
516 
+chr6_mann_hap4	2998915	2998972	-	NR_033489	0
517 
+chr6_mann_hap4	2998915	2998972	-	NM_021160	0
518 
+chr6_mann_hap4	2998915	2998972	-	NR_033488	0
519 
+chr6_mann_hap4	2999389	2999453	-	NM_001177515	0
520 
+chr6_mann_hap4	2999389	2999453	-	NR_033489	0
521 
+chr6_mann_hap4	2999389	2999453	-	NM_021160	0
522 
+chr6_mann_hap4	2999389	2999453	-	NR_033488	0
523 
+chr6_mann_hap4	2999681	2999786	-	NM_001177515	0
524 
+chr6_mann_hap4	2999681	2999786	-	NR_033489	0
525 
+chr6_mann_hap4	2999681	2999786	-	NM_021160	0
526 
+chr6_mann_hap4	2999681	2999786	-	NR_033488	0
527 
+chr6_mann_hap4	3000247	3000371	-	NM_001177515	0
528 
+chr6_mann_hap4	3000247	3000371	-	NR_033489	0
529 
+chr6_mann_hap4	3000247	3000371	-	NM_021160	0
530 
+chr6_mann_hap4	3000247	3000371	-	NR_033488	0
531 
+chr6_mann_hap4	3000744	3000794	-	NM_001177515	0
532 
+chr6_mann_hap4	3000744	3000794	-	NR_033489	0
533 
+chr6_mann_hap4	3000744	3000794	-	NM_021160	0
534 
+chr6_mann_hap4	3000744	3000794	-	NR_033488	0
535 
+chr6_mann_hap4	3001205	3001269	-	NM_001177515	0
536 
+chr6_mann_hap4	3001205	3001269	-	NR_033489	0
537 
+chr6_mann_hap4	3001205	3001269	-	NM_021160	0
538 
+chr6_mann_hap4	3001205	3001269	-	NR_033488	0
539 
+chr6_mann_hap4	3002245	3002347	-	NM_001177515	0
540 
+chr6_mann_hap4	3002245	3002347	-	NR_033489	0
541 
+chr6_mann_hap4	3002245	3002347	-	NM_021160	0
542 
+chr6_mann_hap4	3002245	3002347	-	NR_033488	0
543 
+chr6_mann_hap4	3002470	3002585	-	NM_001177515	0
544 
+chr6_mann_hap4	3002470	3002585	-	NR_033489	0
545 
+chr6_mann_hap4	3002470	3002585	-	NM_021160	0
546 
+chr7	128588263	128588382	+	NM_001098630	0
547 
+chr7	128588263	128588382	+	NM_001242452	0
548 
+chr7	128588263	128588382	+	NM_032643	0
549 
+chr7	128588263	128588382	+	NM_001098627	0
550 
+chr7	128588626	128590096	+	NM_001098629	0
551 
+chr7	128588626	128590096	+	NM_001098630	0
552 
+chr7	128588626	128590096	+	NM_001242452	0
553 
+chr7	128588626	128590096	+	NM_032643	0
554 
+chr7	128588626	128590096	+	NM_001098627	0
555 
+chr7	128594233	128595439	-	NR_034053	0
556 
+chr7	128594233	128595439	-	NM_001191028	0
557 
+chr7	128594233	128595439	-	NM_012470	0
558 
+chr7	128597277	128597369	-	NR_034053	0
559 
+chr7	128597277	128597369	-	NM_001191028	0
560 
+chr7	128597277	128597369	-	NM_012470	0
561 
+chr7	128607333	128607446	-	NR_034053	0
562 
+chr7	128607333	128607446	-	NM_001191028	0
563 
+chr7	128607333	128607446	-	NM_012470	0
564 
+chr7	128610201	128610369	-	NR_034053	0
565 
+chr7	128610201	128610369	-	NM_001191028	0
566 
+chr7	128610201	128610369	-	NM_012470	0
567 
+chr7	128612479	128612636	-	NR_034053	0
568 
+chr7	128612479	128612636	-	NM_001191028	0
569 
+chr7	128612479	128612636	-	NM_012470	0
570 
+chr7	128614921	128615016	-	NR_034053	0
571 
+chr7	128614921	128615016	-	NM_001191028	0
0 572 
\ No newline at end of file
inst/example/DATASET_META/files/S_00000.gdm.meta
History View file @ 54f1b5c
1 573 
new file mode 100755
... ... 
@@ -0,0 +1,9 @@
1 
+annotation_type	exons
2 
+assembly	hg19
3 
+disease	cancer
4 
+disease	pulmonary fibrosis
5 
+disease	Tuberous sclerosis
6 
+disease	neurofibromatosis type 1
7 
+name	RefSeqGeneExons
8 
+original_provider	RefSeq
9 
+provider	POLIMI
inst/example/DATASET_META/files/test.schema
History View file @ 54f1b5c
0 10 
new file mode 100755
... ... 
@@ -0,0 +1,11 @@
1 
+<?xml version='1.0' encoding='UTF-8'?>
2 
+<gmqlSchemaCollection name="job_filename_guest_new1196_20171031_083542_Exon" xmlns="http://genomic.elet.polimi.it/entities">
3 
+	<gmqlSchema type="Peak" coordinate_system="default">
4 
+		<field type="STRING">chr</field>
5 
+		<field type="LONG">left</field>
6 
+		<field type="LONG">right</field>
7 
+		<field type="CHAR">strand</field>
8 
+		<field type="STRING">name</field>
9 
+		<field type="DOUBLE">score</field>
10 
+	</gmqlSchema>
11 
+</gmqlSchemaCollection>
0 12 
\ No newline at end of file
inst/example/DATASET_META/job_filename_guest_new1196_20171031_083542_Exon.gmql
History View file @ 54f1b5c
1 13 
new file mode 100755
... ... 
@@ -0,0 +1,2 @@
1 
+Exon = SELECT(annotation_type == 'exons' AND original_provider == 'RefSeq') HG19_BED_ANNOTATION;
2 
+MATERIALIZE Exon INTO Exon;
0 3 
\ No newline at end of file
inst/example/DATASET_META/vocabulary.txt
History View file @ 54f1b5c
1 4 
new file mode 100755
... ... 
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inst/example/files/S_1.gtf
History View file @ 54f1b5c
0 11 
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... ... 
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+##gff-version 2
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+##source-version rtracklayer 1.36.6
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+##date 2018-01-26
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+chr5	rtracklayer	sequence_feature	133901805	133902270	0	+	.	name "NM_001289984"
410 
+chr5	rtracklayer	sequence_feature	133901805	133902270	0	+	.	name "NM_001289985"
411 
+chr5	rtracklayer	sequence_feature	133909334	133909452	0	+	.	name "NM_015288"
412 
+chr5	rtracklayer	sequence_feature	133909334	133909452	0	+	.	name "NM_001289984"
413 
+chr5	rtracklayer	sequence_feature	133909334	133909452	0	+	.	name "NM_001289985"
414 
+chr5	rtracklayer	sequence_feature	133912457	133912586	0	+	.	name "NM_001289985"
415 
+chr5	rtracklayer	sequence_feature	133914183	133918920	0	+	.	name "NM_001289984"
416 
+chr5	rtracklayer	sequence_feature	133914183	133918920	0	+	.	name "NM_001289985"
417 
+chr5	rtracklayer	sequence_feature	133914186	133918920	0	+	.	name "NM_015288"
418 
+chr5	rtracklayer	sequence_feature	133936838	133942756	0	-	.	name "NM_001033503"
419 
+chr5	rtracklayer	sequence_feature	133936838	133942756	0	-	.	name "NM_016103"
420 
+chr5	rtracklayer	sequence_feature	133944061	133944193	0	-	.	name "NM_001033503"
421 
+chr5	rtracklayer	sequence_feature	133944061	133944193	0	-	.	name "NM_016103"
422 
+chr5	rtracklayer	sequence_feature	133945260	133945364	0	-	.	name "NM_001033503"
423 
+chr5	rtracklayer	sequence_feature	133945260	133945364	0	-	.	name "NM_016103"
424 
+chr5	rtracklayer	sequence_feature	133948380	133948446	0	-	.	name "NM_001033503"
425 
+chr5	rtracklayer	sequence_feature	133948380	133948446	0	-	.	name "NM_016103"
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+chr5	rtracklayer	sequence_feature	133956622	133956742	0	-	.	name "NM_001033503"
427 
+chr5	rtracklayer	sequence_feature	133956622	133956742	0	-	.	name "NM_016103"
428 
+chr5	rtracklayer	sequence_feature	133959651	133959727	0	-	.	name "NM_001033503"
429 
+chr5	rtracklayer	sequence_feature	133959651	133959727	0	-	.	name "NM_016103"
430 
+chr5	rtracklayer	sequence_feature	133967766	133967885	0	-	.	name "NM_001033503"
431 
+chr5	rtracklayer	sequence_feature	133968417	133968533	0	-	.	name "NM_001033503"
432 
+chr5	rtracklayer	sequence_feature	133968417	133968533	0	-	.	name "NM_016103"
433 
+chr5	rtracklayer	sequence_feature	133984474	133984863	0	+	.	name "NM_001252231"
434 
+chr5	rtracklayer	sequence_feature	133984474	133984863	0	+	.	name "NM_021982"
435 
+chr5	rtracklayer	sequence_feature	133996808	133997276	0	+	.	name "NM_001252231"
436 
+chr5	rtracklayer	sequence_feature	133996808	133997276	0	+	.	name "NM_021982"
437 
+chr5	rtracklayer	sequence_feature	134002512	134002686	0	+	.	name "NM_001252231"
438 
+chr5	rtracklayer	sequence_feature	134002512	134002686	0	+	.	name "NM_021982"
439 
+chr5	rtracklayer	sequence_feature	134007498	134007576	0	+	.	name "NM_001252231"
440 
+chr5	rtracklayer	sequence_feature	134007498	134007576	0	+	.	name "NM_021982"
441 
+chr5	rtracklayer	sequence_feature	134010304	134010465	0	+	.	name "NM_001252231"
442 
+chr5	rtracklayer	sequence_feature	134010304	134010465	0	+	.	name "NM_021982"
443 
+chr5	rtracklayer	sequence_feature	134010734	134010907	0	+	.	name "NM_001252231"
444 
+chr5	rtracklayer	sequence_feature	134010734	134010907	0	+	.	name "NM_021982"
445 
+chr5	rtracklayer	sequence_feature	134011712	134011815	0	+	.	name "NM_001252231"
446 
+chr5	rtracklayer	sequence_feature	134011712	134011815	0	+	.	name "NM_021982"
447 
+chr5	rtracklayer	sequence_feature	134015291	134015418	0	+	.	name "NM_001252231"
448 
+chr5	rtracklayer	sequence_feature	134015291	134015418	0	+	.	name "NM_021982"
449 
+chr5	rtracklayer	sequence_feature	134018062	134018172	0	+	.	name "NM_001252231"
450 
+chr5	rtracklayer	sequence_feature	134018062	134018172	0	+	.	name "NM_021982"
451 
+chr5	rtracklayer	sequence_feature	134022479	134022592	0	+	.	name "NM_001252231"
452 
+chr5	rtracklayer	sequence_feature	134022479	134022592	0	+	.	name "NM_021982"
453 
+chr5	rtracklayer	sequence_feature	134023870	134023989	0	+	.	name "NM_001252231"
454 
+chr5	rtracklayer	sequence_feature	134023870	134023989	0	+	.	name "NM_021982"
455 
+chr5	rtracklayer	sequence_feature	134028291	134028347	0	+	.	name "NM_001252231"
456 
+chr5	rtracklayer	sequence_feature	134028291	134028347	0	+	.	name "NM_021982"
457 
+chr8	rtracklayer	sequence_feature	6673378	6673440	0	-	.	name "NM_207411"
458 
+chr8	rtracklayer	sequence_feature	6673378	6673440	0	-	.	name "NM_001289973"
459 
+chr8	rtracklayer	sequence_feature	6679390	6679560	0	-	.	name "NM_207411"
460 
+chr8	rtracklayer	sequence_feature	6679390	6679560	0	-	.	name "NM_001289973"
461 
+chr8	rtracklayer	sequence_feature	6681042	6681252	0	-	.	name "NM_207411"
462 
+chr8	rtracklayer	sequence_feature	6681042	6681252	0	-	.	name "NM_001289973"
463 
+chr8	rtracklayer	sequence_feature	6682686	6682871	0	-	.	name "NM_207411"
464 
+chr8	rtracklayer	sequence_feature	6682686	6682871	0	-	.	name "NM_001289973"
465 
+chr8	rtracklayer	sequence_feature	6686690	6686828	0	-	.	name "NM_001289973"
466 
+chr8	rtracklayer	sequence_feature	6690238	6690422	0	-	.	name "NM_207411"
467 
+chr8	rtracklayer	sequence_feature	6690238	6690422	0	-	.	name "NM_001289973"
468 
+chr8	rtracklayer	sequence_feature	6692957	6693166	0	-	.	name "NM_207411"
469 
+chr8	rtracklayer	sequence_feature	6692957	6693166	0	-	.	name "NM_001289973"
470 
+chr8	rtracklayer	sequence_feature	6693075	6693139	0	+	.	name "NR_045217"
471 
+chr8	rtracklayer	sequence_feature	6693487	6693743	0	+	.	name "NR_045217"
472 
+chr8	rtracklayer	sequence_feature	6699189	6699975	0	+	.	name "NR_045217"
473 
+chr8	rtracklayer	sequence_feature	6728096	6728348	0	-	.	name "NM_005218"
474 
+chr8	rtracklayer	sequence_feature	6735318	6735529	0	-	.	name "NM_005218"
475 
+chr8	rtracklayer	sequence_feature	6782215	6782449	0	-	.	name "NM_001926"
476 
+chr8	rtracklayer	sequence_feature	6783364	6783598	0	-	.	name "NM_001926"
477 
+chr8	rtracklayer	sequence_feature	6793344	6793663	0	-	.	name "NM_001925"
478 
+chr8	rtracklayer	sequence_feature	6794249	6794433	0	-	.	name "NM_001925"
479 
+chr8	rtracklayer	sequence_feature	6795747	6795786	0	-	.	name "NM_001925"
480 
+chr8	rtracklayer	sequence_feature	6808247	6808360	0	-	.	name "NR_073407"
481 
+chr8	rtracklayer	sequence_feature	6808949	6809121	0	-	.	name "NR_073407"
482 
+chr8	rtracklayer	sequence_feature	6816810	6816923	0	-	.	name "NR_073408"
483 
+chr8	rtracklayer	sequence_feature	6817511	6817683	0	-	.	name "NR_073408"
484 
+chr8	rtracklayer	sequence_feature	6825662	6825769	0	-	.	name "NR_029386"
485 
+chr8	rtracklayer	sequence_feature	6826451	6826635	0	-	.	name "NR_029386"
486 
+chr8	rtracklayer	sequence_feature	6835170	6835401	0	-	.	name "NM_004084"
487 
+chr8	rtracklayer	sequence_feature	6835170	6835401	0	-	.	name "NM_001042500"
488 
+chr8	rtracklayer	sequence_feature	6835981	6836168	0	-	.	name "NM_004084"
489 
+chr8	rtracklayer	sequence_feature	6835981	6836168	0	-	.	name "NM_001042500"
490 
+chr8	rtracklayer	sequence_feature	6837534	6837614	0	-	.	name "NM_004084"
491 
+chr8	rtracklayer	sequence_feature	6837534	6837614	0	-	.	name "NM_001042500"
492 
+chr8	rtracklayer	sequence_feature	6844699	6844945	0	-	.	name "NR_036687"
493 
+chr8	rtracklayer	sequence_feature	6844699	6844945	0	-	.	name "NR_036686"
494 
+chr8	rtracklayer	sequence_feature	6845621	6845808	0	-	.	name "NR_036687"
495 
+chr8	rtracklayer	sequence_feature	6845621	6845808	0	-	.	name "NR_036686"
496 
+chr8	rtracklayer	sequence_feature	6847180	6847243	0	-	.	name "NR_036687"
497 
+chr8	rtracklayer	sequence_feature	6847180	6847243	0	-	.	name "NR_036686"
498 
+chr8	rtracklayer	sequence_feature	6854287	6854518	0	-	.	name "NM_004084"
499 
+chr8	rtracklayer	sequence_feature	6854287	6854518	0	-	.	name "NM_001042500"
500 
+chr8	rtracklayer	sequence_feature	6855098	6855285	0	-	.	name "NM_004084"
501 
+chr8	rtracklayer	sequence_feature	6855098	6855285	0	-	.	name "NM_001042500"
502 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998164	2998211	0	-	.	name "NM_001177515"
503 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998164	2998211	0	-	.	name "NR_033489"
504 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998164	2998211	0	-	.	name "NM_021160"
505 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998164	2998211	0	-	.	name "NR_033488"
506 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998308	2998407	0	-	.	name "NM_001177515"
507 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998308	2998407	0	-	.	name "NR_033489"
508 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998308	2998407	0	-	.	name "NM_021160"
509 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998308	2998407	0	-	.	name "NR_033488"
510 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998490	2998567	0	-	.	name "NM_001177515"
511 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998490	2998567	0	-	.	name "NR_033489"
512 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998490	2998567	0	-	.	name "NM_021160"
513 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998490	2998567	0	-	.	name "NR_033488"
514 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998707	2998770	0	-	.	name "NM_001177515"
515 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998707	2998770	0	-	.	name "NR_033489"
516 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998707	2998770	0	-	.	name "NM_021160"
517 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998707	2998770	0	-	.	name "NR_033488"
518 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998915	2998972	0	-	.	name "NM_001177515"
519 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998915	2998972	0	-	.	name "NR_033489"
520 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998915	2998972	0	-	.	name "NM_021160"
521 
+chr6_mann_hap4	rtracklayer	sequence_feature	2998915	2998972	0	-	.	name "NR_033488"
522 
+chr6_mann_hap4	rtracklayer	sequence_feature	2999389	2999453	0	-	.	name "NM_001177515"
523 
+chr6_mann_hap4	rtracklayer	sequence_feature	2999389	2999453	0	-	.	name "NR_033489"
524 
+chr6_mann_hap4	rtracklayer	sequence_feature	2999389	2999453	0	-	.	name "NM_021160"
525 
+chr6_mann_hap4	rtracklayer	sequence_feature	2999389	2999453	0	-	.	name "NR_033488"
526 
+chr6_mann_hap4	rtracklayer	sequence_feature	2999681	2999786	0	-	.	name "NM_001177515"
527 
+chr6_mann_hap4	rtracklayer	sequence_feature	2999681	2999786	0	-	.	name "NR_033489"
528 
+chr6_mann_hap4	rtracklayer	sequence_feature	2999681	2999786	0	-	.	name "NM_021160"
529 
+chr6_mann_hap4	rtracklayer	sequence_feature	2999681	2999786	0	-	.	name "NR_033488"
530 
+chr6_mann_hap4	rtracklayer	sequence_feature	3000247	3000371	0	-	.	name "NM_001177515"
531 
+chr6_mann_hap4	rtracklayer	sequence_feature	3000247	3000371	0	-	.	name "NR_033489"
532 
+chr6_mann_hap4	rtracklayer	sequence_feature	3000247	3000371	0	-	.	name "NM_021160"
533 
+chr6_mann_hap4	rtracklayer	sequence_feature	3000247	3000371	0	-	.	name "NR_033488"
534 
+chr6_mann_hap4	rtracklayer	sequence_feature	3000744	3000794	0	-	.	name "NM_001177515"
535 
+chr6_mann_hap4	rtracklayer	sequence_feature	3000744	3000794	0	-	.	name "NR_033489"
536 
+chr6_mann_hap4	rtracklayer	sequence_feature	3000744	3000794	0	-	.	name "NM_021160"
537 
+chr6_mann_hap4	rtracklayer	sequence_feature	3000744	3000794	0	-	.	name "NR_033488"
538 
+chr6_mann_hap4	rtracklayer	sequence_feature	3001205	3001269	0	-	.	name "NM_001177515"
539 
+chr6_mann_hap4	rtracklayer	sequence_feature	3001205	3001269	0	-	.	name "NR_033489"
540 
+chr6_mann_hap4	rtracklayer	sequence_feature	3001205	3001269	0	-	.	name "NM_021160"
541 
+chr6_mann_hap4	rtracklayer	sequence_feature	3001205	3001269	0	-	.	name "NR_033488"
542 
+chr6_mann_hap4	rtracklayer	sequence_feature	3002245	3002347	0	-	.	name "NM_001177515"
543 
+chr6_mann_hap4	rtracklayer	sequence_feature	3002245	3002347	0	-	.	name "NR_033489"
544 
+chr6_mann_hap4	rtracklayer	sequence_feature	3002245	3002347	0	-	.	name "NM_021160"
545 
+chr6_mann_hap4	rtracklayer	sequence_feature	3002245	3002347	0	-	.	name "NR_033488"
546 
+chr6_mann_hap4	rtracklayer	sequence_feature	3002470	3002585	0	-	.	name "NM_001177515"
547 
+chr6_mann_hap4	rtracklayer	sequence_feature	3002470	3002585	0	-	.	name "NR_033489"
548 
+chr6_mann_hap4	rtracklayer	sequence_feature	3002470	3002585	0	-	.	name "NM_021160"
549 
+chr7	rtracklayer	sequence_feature	128588263	128588382	0	+	.	name "NM_001098630"
550 
+chr7	rtracklayer	sequence_feature	128588263	128588382	0	+	.	name "NM_001242452"
551 
+chr7	rtracklayer	sequence_feature	128588263	128588382	0	+	.	name "NM_032643"
552 
+chr7	rtracklayer	sequence_feature	128588263	128588382	0	+	.	name "NM_001098627"
553 
+chr7	rtracklayer	sequence_feature	128588626	128590096	0	+	.	name "NM_001098629"
554 
+chr7	rtracklayer	sequence_feature	128588626	128590096	0	+	.	name "NM_001098630"
555 
+chr7	rtracklayer	sequence_feature	128588626	128590096	0	+	.	name "NM_001242452"
556 
+chr7	rtracklayer	sequence_feature	128588626	128590096	0	+	.	name "NM_032643"
557 
+chr7	rtracklayer	sequence_feature	128588626	128590096	0	+	.	name "NM_001098627"
558 
+chr7	rtracklayer	sequence_feature	128594233	128595439	0	-	.	name "NR_034053"
559 
+chr7	rtracklayer	sequence_feature	128594233	128595439	0	-	.	name "NM_001191028"
560 
+chr7	rtracklayer	sequence_feature	128594233	128595439	0	-	.	name "NM_012470"
561 
+chr7	rtracklayer	sequence_feature	128597277	128597369	0	-	.	name "NR_034053"
562 
+chr7	rtracklayer	sequence_feature	128597277	128597369	0	-	.	name "NM_001191028"
563 
+chr7	rtracklayer	sequence_feature	128597277	128597369	0	-	.	name "NM_012470"
564 
+chr7	rtracklayer	sequence_feature	128607333	128607446	0	-	.	name "NR_034053"
565 
+chr7	rtracklayer	sequence_feature	128607333	128607446	0	-	.	name "NM_001191028"
566 
+chr7	rtracklayer	sequence_feature	128607333	128607446	0	-	.	name "NM_012470"
567 
+chr7	rtracklayer	sequence_feature	128610201	128610369	0	-	.	name "NR_034053"
568 
+chr7	rtracklayer	sequence_feature	128610201	128610369	0	-	.	name "NM_001191028"
569 
+chr7	rtracklayer	sequence_feature	128610201	128610369	0	-	.	name "NM_012470"
570 
+chr7	rtracklayer	sequence_feature	128612479	128612636	0	-	.	name "NR_034053"
571 
+chr7	rtracklayer	sequence_feature	128612479	128612636	0	-	.	name "NM_001191028"
572 
+chr7	rtracklayer	sequence_feature	128612479	128612636	0	-	.	name "NM_012470"
573 
+chr7	rtracklayer	sequence_feature	128614921	128615016	0	-	.	name "NR_034053"
574 
+chr7	rtracklayer	sequence_feature	128614921	128615016	0	-	.	name "NM_001191028"
inst/example/files/S_1.gtf.meta
History View file @ 54f1b5c
0 575 
new file mode 100644
... ... 
@@ -0,0 +1,5 @@
1 
+annotation_type	exons
2 
+assembly	hg19
3 
+name	RefSeqGeneExons
4 
+original_provider	RefSeq
5 
+provider	POLIMI
inst/example/files/granges.schema
History View file @ 54f1b5c
0 6 
new file mode 100644
... ... 
@@ -0,0 +1,14 @@
1 
+<?xml version="1.0" encoding="UTF-8"?>
2 
+<gmqlSchemaCollection xmlns="http://genomic.elet.polimi.it/entities" name="DatasetName_SCHEMAS">
3 
+  <gmqlSchema>
4 
+    <field type="STRING">seqname</field>
5 
+    <field type="STRING">source</field>
6 
+    <field type="STRING">feature</field>
7 
+    <field type="LONG">start</field>
8 
+    <field type="LONG">end</field>
9 
+    <field type="DOUBLE">score</field>
10 
+    <field type="STRING">strand</field>
11 
+    <field type="STRING">frame</field>
12 
+    <field type="STRING">name</field>
13 
+  </gmqlSchema>
14 
+</gmqlSchemaCollection>
vignettes/RGMQL-vignette.Rmd
History View file @ 54f1b5c
... ... 
@@ -748,14 +748,64 @@ Note that this function works only if every sample in dataset includes the
748 748 
 same number of regions with the same coordinates.
749 749 
 Each metadata column is named using *region_attributes* concatenated with
750 750 
 the function input parameter *suffix*.
751 
-By default *suffix* correspond to a metadata: *antobody_target*.
751 
+By default *suffix* correspond to a metadata: *antibody_target*.
752 752
753 753 
 ## Metadata
754 754
755 
-A specific metadata attribute, associated to sample of GMQL dataset, can
756 
-contain mmultiple values, i.e more values for the same metadata-key attributes;
757 
-es:
755 
+Eache sample of GMQL dataset has its own metadata associated and generally
756 
+every metadata has a single value. In case we got mutiple distinct values
757 
+for the same metadata-key attributes, as showed in the figure below:
758 
+\newline
759 
+![metadata with multiple values](multi_metadata.png)
760 
+\newline\newline
761 
+In this case we have multiple values for metadata *disease*; GMQL auomcatically
762 
+handle this 'issue'.
763 
+In the import/export paragrapgh we showed that the GMQL dataset can be
764 
+imported and so its metadata too.
765 
+
766 
+```{r, metadata}
767 
+# This statement defines the path to the folder "EXON" in the subdirectory
768 
+# "example" of the package "RGMQL"
758 769
770 
+dataset_path <- system.file("example", "DATASET_META", package = "RGMQL")
759 771
760 
-# References
772 
+# Import the GMQL dataset DATASET_META as GRangesList
773 
+
774 
+grl_data <- import_gmql(dataset_path, is_gtf = FALSE)
775 
+grl_data
776 
+
777 
+# and its metadata
778 
+
779 
+metadata(grl_data)
780 
+
781 
+```
782 
+The metadata is stored as simple list in the form key-values and it doesn't
783 
+matter if mutiple values for one metadata-key attribute are present; all values
784 
+are stored and showed.
785 
+The problem is raised once we need to get the metadata value; normally since
786 
+listis in the form key-value we can extract the metadata value using:
787 
+
788 
+```{r, retrieve_value}
789 
+
790 
+# stored metadata on variable a
791 
+
792 
+a = metadata(grl_data)
761 793
794 
+# get disease value of sample S_00000
795 
+
796 
+a$S_00000$disease
797 
+
798 
+```
799 
+In this case only the first value is showed. If we would retrieve all disease,
800 
+we should use:
801 
+
802 
+```{r, retrieve_values}
803 
+
804 
+# get all disease value of sample S_00000
805 
+
806 
+a$S_00000[which(names(a$S_00000) %in% "disease")]
807 
+
808 
+```
809 
+
810 
+
811 
+# References
vignettes/multi_metadata.png
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