|
54
|
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") {
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|
|
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,
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342 orderByLocation = TRUE)
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343 locusNames <- names(gr)
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344 sampleNames(gset) <- gset$title
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345 common <- intersect(locusNames, fData(gset)$Name)
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346 if (length(common) == 0)
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347 stop("No rowname matches. 'rownames' need to match IlluminaHumanMethylation450k probe names.")
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348 ind1 <- match(common, fData(gset)$Name)
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349 ind2 <- match(common, locusNames)
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350 preprocessing <- c(rg.norm = paste0("See GEO ", GSE, " for details"))
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351 if (what == "Beta") {
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352 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = exprs(gset)[ind1,
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353 , drop = FALSE], M = NULL, CN = NULL, pData = pData(gset),
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354 annotation = c(array = array, annotation = annotation),
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355 preprocessMethod = preprocessing)
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356 }
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357 else {
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358 out <- GenomicRatioSet(gr = gr[ind2, ], Beta = NULL,
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359 M = exprs(gset)[ind1, , drop = FALSE], CN = NULL,
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360 pData = pData(gset), annotation = c(array = array,
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361 annotation = annotation), preprocessMethod = preprocessing)
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362 }
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363 save(out,output)
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364 }
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365 getwd()
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366 GSE <- "GSE51547"
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367 output <- ("out.Rdata")
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368 require("BiocGenerics", quietly = TRUE)
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369 require("data.table", quietly = TRUE)
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370 require("GEOquery", quietly = TRUE)
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371 require("rtracklayer", quietly = TRUE)
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372 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
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373 require("minfi", quietly = TRUE)
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374 GSE <- "GSE51547"
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375 output <- ("out.Rdata")
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376 function (GSE = NULL, path = NULL, array = "IlluminaHumanMethylation450k",
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377 annotation = .default.450k.annotation, what = c("Beta", "M"),
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378 mergeManifest = FALSE, i = 1)
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379 {
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380 what <- match.arg(what)
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381 if (is.null(GSE) && is.null(path))
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382 stop("Either GSE or path must be supplied.")
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383 if (!is.null(GSE))
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384 gset <- GEOquery::getGEO(GSE)
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385 else gset <- GEOquery::getGEO(filename = file.path(path,
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386 list.files(path, pattern = ".soft")))
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387 if (length(gset) == 0)
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388 stop("Empty list retrieved from GEO.")
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389 if (length(gset) > 1) {
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390 warning("More than one ExpressionSet found:\n", names(gset),
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391 "\nUsing entry ", i)
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392 gset <- gset[[i]]
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393 }
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394 else gset <- gset[[1]]
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395 platform <- annotation(gset)
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396 if (platform != "GPL13534")
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397 warning(sprintf("%s is not the platform ID associated with IlluminaHumanMethylation450k. Should be GPL13534.",
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398 platform))
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399 if (what == "Beta" & (min(exprs(gset)[, 1], na.rm = TRUE) <
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400 0 | max(exprs(gset)[, 1], na.rm = TRUE) > 1))
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401 warning("Values outside [0,1] detected. 'what' argument should not be Beta.")
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402 ann <- .getAnnotationString(c(array = array, annotation = annotation))
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403 if (!require(ann, character.only = TRUE))
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404 stop(sprintf("cannot load annotation package %s", ann))
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405 object <- get(ann)
|
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406 gr <- getLocations(object, mergeManifest = mergeManifest,
|
|
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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)
|
