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comparison getGEO/test-data/.Rhistory @ 65:ad054b925eda draft

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author testtool
date Thu, 11 May 2017 06:31:45 -0400
parents 7aab6e28c62e
children
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64:e8ea94f5f273 65:ad054b925eda
1 what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
2 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1)
3 ??getLocations
4 sampleNames(gset) <- gset$title
5 if (platform != "GPL13534")
6 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
7 platform))
8 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
9 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
10 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
11 ann <- .getAnnotationString(c(array = array, annotation = annotation))
12 if (!require(ann, character.only = TRUE))
13 stop(sprintf("cannot load annotation package %s", ann))
14 getGenomicRatioSetFromGEO
15 object <- get(platform)
16 platform
17 gr <- getLocations(gset, mergeManifest = mergeManifest,
18 orderByLocation = TRUE)
19 gr <- getLocations(gset)
20 gset
21 gr <- getLocations(platform)
22 ??getLocations
23 locusNames <- names(gset)
24 sampleNames(gset) <- gset$title
25 common <- intersect(locusNames, fData(gset)$Name)
26 if (length(common) == 0)
27 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
28 ind1 <- match(common, fData(gset)$Name)
29 ind2 <- match(common, locusNames)
30 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
31 if (what == "Beta") {
32 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
33 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
34 annotation = c(array = array, annotation = annotation),
35 preprocessMethod = preprocessing)
36 }
37 what
38 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
39 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
40 annotation = c(array = array, annotation = annotation),
41 preprocessMethod = preprocessing)
42 out <- GenomicRatioSet(gr = gset[ind2, ], Beta = exprs(gset)[ind1,
43 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
44 annotation = c(array = array, annotation = annotation),
45 preprocessMethod = preprocessing)
46 ind2
47 ind1
48 common
49 sampleNames(gset)
50 class(gmSet)
51 out <- GenomicRatioSet(gr = gmset, Beta = exprs(gset)[ind1,
52 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
53 annotation = c(array = array, annotation = annotation),
54 preprocessMethod = preprocessing)
55 if (length(TAB$ID) > 1) {
56 mysamples <-
57 do.call("data.table", lapply(TAB$ID[-1], function(x)
58 Table(getGEO(x, getGPL = FALSE))[, -1]))
59 gmSet <- data.table(IlmnIDTable[, -1], mysamples)
60 } else {
61 gmSet <- Table(getGEO(TAB$ID, getGPL = FALSE))
62 }
63 out <- GenomicRatioSet(gr = gmset, Beta = exprs(gset)[ind1,
64 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
65 annotation = c(array = array, annotation = annotation),
66 preprocessMethod = preprocessing)
67 out <- GenomicRatioSet(gr = gmSet, Beta = exprs(gset)[ind1,
68 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
69 annotation = c(array = array, annotation = annotation),
70 preprocessMethod = preprocessing)
71 ??GenomicRatioSet
72 sampleNames(gset)
73 common
74 class(gset)
75 ??GenomicRatioSet
76 GenomicRatioSet
77 getGenomicRatioSetFromGEO
78 GSE <- "GSE51547"
79 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
80 annotation = .default.450k.annotation, what = c("Beta", "M"),
81 mergeManifest = FALSE, i = 1)
82 {
83 what <- match.arg(what)
84 if (is.null(GSE) && is.null(path))
85 stop("Either GSE or path must be supplied.")
86 if (!is.null(GSE))
87 gset <- GEOquery::getGEO(GSE)
88 else gset <- GEOquery::getGEO(filename = file.path(path,
89 list.files(path, pattern = ".soft")))
90 if (length(gset) == 0)
91 stop("Empty list retrieved from GEO.")
92 if (length(gset) > 1) {
93 warning("More than one ExpressionSet found:\n", names(gset),
94 "\nUsing entry ", i)
95 gset <- gset[[i]]
96 }
97 else gset <- gset[[1]]
98 platform <- annotation(gset)
99 if (platform != "GPL13534")
100 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
101 platform))
102 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
103 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
104 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
105 ann <- .getAnnotationString(c(array = array, annotation = annotation))
106 if (!require(ann, character.only = TRUE))
107 stop(sprintf("cannot load annotation package %s", ann))
108 object <- get(ann)
109 gr <- getLocations(object, mergeManifest = mergeManifest,
110 orderByLocation = TRUE)
111 locusNames <- names(gr)
112 sampleNames(gset) <- gset$title
113 common <- intersect(locusNames, fData(gset)$Name)
114 if (length(common) == 0)
115 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
116 ind1 <- match(common, fData(gset)$Name)
117 ind2 <- match(common, locusNames)
118 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
119 if (what == "Beta") {
120 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
121 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
122 annotation = c(array = array, annotation = annotation),
123 preprocessMethod = preprocessing)
124 }
125 else {
126 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
127 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
128 pData = pData(gset), annotation = c(array = array,
129 annotation = annotation), preprocessMethod = preprocessing)
130 }
131 return(out)
132 }
133 out
134 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
135 annotation = .default.450k.annotation, what = c("Beta", "M"),
136 mergeManifest = FALSE, i = 1)
137 {
138 what <- match.arg(what)
139 if (is.null(GSE) && is.null(path))
140 stop("Either GSE or path must be supplied.")
141 if (!is.null(GSE))
142 gset <- GEOquery::getGEO(GSE)
143 else gset <- GEOquery::getGEO(filename = file.path(path,
144 list.files(path, pattern = ".soft")))
145 if (length(gset) == 0)
146 stop("Empty list retrieved from GEO.")
147 if (length(gset) > 1) {
148 warning("More than one ExpressionSet found:\n", names(gset),
149 "\nUsing entry ", i)
150 gset <- gset[[i]]
151 }
152 GSE <- "GSE51547"
153 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
154 annotation = .default.450k.annotation, what = c("Beta", "M"),
155 mergeManifest = FALSE, i = 1)
156 {
157 what <- match.arg(what)
158 if (is.null(GSE) && is.null(path))
159 stop("Either GSE or path must be supplied.")
160 if (!is.null(GSE))
161 gset <- GEOquery::getGEO(GSE)
162 else gset <- GEOquery::getGEO(filename = file.path(path,
163 list.files(path, pattern = ".soft")))
164 if (length(gset) == 0)
165 stop("Empty list retrieved from GEO.")
166 if (length(gset) > 1) {
167 warning("More than one ExpressionSet found:\n", names(gset),
168 "\nUsing entry ", i)
169 gset <- gset[[i]]
170 }
171 else gset <- gset[[1]]
172 platform <- annotation(gset)
173 if (platform != "GPL13534")
174 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
175 platform))
176 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
177 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
178 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
179 ann <- .getAnnotationString(c(array = array, annotation = annotation))
180 if (!require(ann, character.only = TRUE))
181 stop(sprintf("cannot load annotation package %s", ann))
182 object <- get(ann)
183 gr <- getLocations(object, mergeManifest = mergeManifest,
184 orderByLocation = TRUE)
185 locusNames <- names(gr)
186 sampleNames(gset) <- gset$title
187 common <- intersect(locusNames, fData(gset)$Name)
188 if (length(common) == 0)
189 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
190 ind1 <- match(common, fData(gset)$Name)
191 ind2 <- match(common, locusNames)
192 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
193 if (what == "Beta") {
194 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
195 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
196 annotation = c(array = array, annotation = annotation),
197 preprocessMethod = preprocessing)
198 }
199 else {
200 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
201 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
202 pData = pData(gset), annotation = c(array = array,
203 annotation = annotation), preprocessMethod = preprocessing)
204 }
205 return(out)
206 }
207 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
208 annotation = .default.450k.annotation, what = c("Beta", "M"),
209 mergeManifest = FALSE, i = 1)
210 {
211 what <- match.arg(what)
212 if (is.null(GSE) && is.null(path))
213 stop("Either GSE or path must be supplied.")
214 if (!is.null(GSE))
215 gset <- GEOquery::getGEO(GSE)
216 else gset <- GEOquery::getGEO(filename = file.path(path,
217 list.files(path, pattern = ".soft")))
218 if (length(gset) == 0)
219 stop("Empty list retrieved from GEO.")
220 if (length(gset) > 1) {
221 warning("More than one ExpressionSet found:\n", names(gset),
222 "\nUsing entry ", i)
223 gset <- gset[[i]]
224 }
225 else gset <- gset[[1]]
226 platform <- annotation(gset)
227 if (platform != "GPL13534")
228 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
229 platform))
230 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
231 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
232 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
233 ann <- .getAnnotationString(c(array = array, annotation = annotation))
234 if (!require(ann, character.only = TRUE))
235 stop(sprintf("cannot load annotation package %s", ann))
236 object <- get(ann)
237 gr <- getLocations(object, mergeManifest = mergeManifest,
238 orderByLocation = TRUE)
239 locusNames <- names(gr)
240 sampleNames(gset) <- gset$title
241 common <- intersect(locusNames, fData(gset)$Name)
242 if (length(common) == 0)
243 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
244 ind1 <- match(common, fData(gset)$Name)
245 ind2 <- match(common, locusNames)
246 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
247 if (what == "Beta") {
248 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
249 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
250 annotation = c(array = array, annotation = annotation),
251 preprocessMethod = preprocessing)
252 }
253 else {
254 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
255 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
256 pData = pData(gset), annotation = c(array = array,
257 annotation = annotation), preprocessMethod = preprocessing)
258 }
259 return(out)
260 }
261 return(out)
262 }
263 what <- match.arg(what)
264 if (length(gset) == 0)
265 stop("Empty list retrieved from GEO.")
266 if (length(gset) > 1) {
267 warning("More than one ExpressionSet found:\n", names(gset),
268 "\nUsing entry ", i)
269 gset <- gset[[i]]
270 }
271 else gset <- gset[[1]]
272 platform <- annotation(gset)
273 if (platform != "GPL13534")
274 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
275 platform))
276 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
277 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
278 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
279 what
280 platform <- annotation(gset)
281 if (platform != "GPL13534")
282 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
283 platform))
284 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
285 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
286 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
287 ann <- .getAnnotationString(c(array = array, annotation = annotation))
288 if (!require(ann, character.only = TRUE))
289 stop(sprintf("cannot load annotation package %s", ann))
290 object <- get(ann)
291 gr <- getLocations(object, mergeManifest = mergeManifest,
292 orderByLocation = TRUE)
293 ann <- .getAnnotationString(c(array = array, annotation = annotation))
294 ann <- .getAnnotationString(c(array = array, annotation = annotation))
295 ??getLocations
296 getAnnotation(gset, what = "everything", lociNames = NULL,
297 orderByLocation = FALSE, dropNonMapping = FALSE)
298 ann <- getAnnotation(gset)
299 GEODataTable
300 IlmnIDTable
301 matrix<- as.matrix(gmSet)
302 matrix
303 gr<- GRanges(matrix)
304 IlmnIDTable
305 GEODataTable
306 getGenomicRatioSetFromGEO
307 require("minfi", quietly = TRUE)
308 args <- commandArgs(trailingOnly = TRUE)
309 GSE = args[1]
310 output = args[2]
311 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
312 annotation = .default.450k.annotation, what = c("Beta", "M"),
313 mergeManifest = FALSE, i = 1)
314 {
315 what <- match.arg(what)
316 if (is.null(GSE) && is.null(path))
317 stop("Either GSE or path must be supplied.")
318 if (!is.null(GSE))
319 gset <- GEOquery::getGEO(GSE)
320 else gset <- GEOquery::getGEO(filename = file.path(path,
321 list.files(path, pattern = ".soft")))
322 if (length(gset) == 0)
323 stop("Empty list retrieved from GEO.")
324 if (length(gset) > 1) {
325 warning("More than one ExpressionSet found:\n", names(gset),
326 "\nUsing entry ", i)
327 gset <- gset[[i]]
328 }
329 else gset <- gset[[1]]
330 platform <- annotation(gset)
331 if (platform != "GPL13534")
332 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
333 platform))
334 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
335 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
336 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
337 ann <- .getAnnotationString(c(array = array, annotation = annotation))
338 if (!require(ann, character.only = TRUE))
339 stop(sprintf("cannot load annotation package %s", ann))
340 object <- get(ann)
341 gr <- getLocations(object, mergeManifest = mergeManifest,
342 orderByLocation = TRUE)
343 locusNames <- names(gr)
344 sampleNames(gset) <- gset$title
345 common <- intersect(locusNames, fData(gset)$Name)
346 if (length(common) == 0)
347 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
348 ind1 <- match(common, fData(gset)$Name)
349 ind2 <- match(common, locusNames)
350 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
351 if (what == "Beta") {
352 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
353 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
354 annotation = c(array = array, annotation = annotation),
355 preprocessMethod = preprocessing)
356 }
357 else {
358 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
359 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
360 pData = pData(gset), annotation = c(array = array,
361 annotation = annotation), preprocessMethod = preprocessing)
362 }
363 save(out,output)
364 }
365 getwd()
366 GSE <- "GSE51547"
367 output <- ("out.Rdata")
368 require("BiocGenerics", quietly = TRUE)
369 require("data.table", quietly = TRUE)
370 require("GEOquery", quietly = TRUE)
371 require("rtracklayer", quietly = TRUE)
372 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
373 require("minfi", quietly = TRUE)
374 GSE <- "GSE51547"
375 output <- ("out.Rdata")
376 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
377 annotation = .default.450k.annotation, what = c("Beta", "M"),
378 mergeManifest = FALSE, i = 1)
379 {
380 what <- match.arg(what)
381 if (is.null(GSE) && is.null(path))
382 stop("Either GSE or path must be supplied.")
383 if (!is.null(GSE))
384 gset <- GEOquery::getGEO(GSE)
385 else gset <- GEOquery::getGEO(filename = file.path(path,
386 list.files(path, pattern = ".soft")))
387 if (length(gset) == 0)
388 stop("Empty list retrieved from GEO.")
389 if (length(gset) > 1) {
390 warning("More than one ExpressionSet found:\n", names(gset),
391 "\nUsing entry ", i)
392 gset <- gset[[i]]
393 }
394 else gset <- gset[[1]]
395 platform <- annotation(gset)
396 if (platform != "GPL13534")
397 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
398 platform))
399 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
400 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
401 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
402 ann <- .getAnnotationString(c(array = array, annotation = annotation))
403 if (!require(ann, character.only = TRUE))
404 stop(sprintf("cannot load annotation package %s", ann))
405 object <- get(ann)
406 gr <- getLocations(object, mergeManifest = mergeManifest,
407 orderByLocation = TRUE)
408 locusNames <- names(gr)
409 sampleNames(gset) <- gset$title
410 common <- intersect(locusNames, fData(gset)$Name)
411 if (length(common) == 0)
412 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
413 ind1 <- match(common, fData(gset)$Name)
414 ind2 <- match(common, locusNames)
415 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
416 if (what == "Beta") {
417 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
418 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
419 annotation = c(array = array, annotation = annotation),
420 preprocessMethod = preprocessing)
421 }
422 else {
423 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
424 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
425 pData = pData(gset), annotation = c(array = array,
426 annotation = annotation), preprocessMethod = preprocessing)
427 }
428 save(out,output)
429 }
430 out
431 what
432 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
433 annotation = .default.450k.annotation, what = c("Beta", "M"),
434 mergeManifest = FALSE, i = 1)
435 what <- match.arg(what)
436 if (length(gset) == 0)
437 stop("Empty list retrieved from GEO.")
438 if (length(gset) > 1) {
439 warning("More than one ExpressionSet found:\n", names(gset),
440 "\nUsing entry ", i)
441 gset <- gset[[i]]
442 if (length(gset) == 0) {
443 stop("Empty list retrieved from GEO.")
444 } if (length(gset) > 1) {
445 warning("More than one ExpressionSet found:\n", names(gset),
446 "\nUsing entry ", i)}
447 if (length(gset) == 0)
448 stop("Empty list retrieved from GEO.")
449 if (length(gset) > 1) {
450 warning("More than one ExpressionSet found:\n", names(gset),
451 "\nUsing entry ", i)
452 gset <- gset[[i]]}
453 gset
454 else gset <- gset[[1]]
455 gset <- gset[[1]]
456 gset
457 gset <- gset[[i]]}
458 gset <- getGEO(GSE)
459 1gset <- gset[[i]]
460 if (length(gset) == 0)
461 stop("Empty list retrieved from GEO.")
462 if (length(gset) > 1) {
463 warning("More than one ExpressionSet found:\n", names(gset),
464 "\nUsing entry ", i)
465 1gset <- gset[[i]]
466 if (length(gset) == 0)
467 stop("Empty list retrieved from GEO.")
468 if (length(gset) > 1) {
469 warning("More than one ExpressionSet found:\n", names(gset),
470 "\nUsing entry ", i)
471 1gset <- gset[[i]]
472 if (length(gset) == 0)
473 stop("Empty list retrieved from GEO.")
474 if (length(gset) > 1) {
475 warning("More than one ExpressionSet found:\n", names(gset),
476 "\nUsing entry ", i)
477 gset <- gset[[i]]
478 if (length(gset) == 0)
479 stop("Empty list retrieved from GEO.")
480 if (length(gset) > 1) {
481 warning("More than one ExpressionSet found:\n", names(gset),
482 "\nUsing entry ", i)
483 gset <- gset[[i]]}
484 if (length(gset) == 0)
485 stop("Empty list retrieved from GEO.")
486 if (length(gset) > 1) {
487 warning("More than one ExpressionSet found:\n", names(gset),
488 "\nUsing entry ", i)
489 gset <- gset[[i]]}
490 if (length(gset) == 0) {
491 stop("Empty list retrieved from GEO.")
492 if (length(gset) > 1) {
493 warning("More than one ExpressionSet found:\n", names(gset),
494 "\nUsing entry ", i)
495 gset <- gset[[i]]}}
496 if (length(gset) == 0) {
497 stop("Empty list retrieved from GEO.")
498 if (length(gset) > 1) {
499 warning("More than one ExpressionSet found:\n", names(gset),
500 "\nUsing entry ", i)
501 gset <- gset[[i]]}}}
502 # else
503 gset
504 class(gset)
505 ann <- .getAnnotationString(c(array = array, annotation = annotation))
506 .getAnnotationString
507 getAnnotationString
508 ??annotation
509 ann <- .getAnnotationString(c(array = array, annotation = annotation))
510 if (!require(ann, character.only = TRUE))
511 stop(sprintf("cannot load annotation package %s", ann))
512 object <- get(ann)