Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/ReadMspDirectory.R
Reads in all .msp
files within a directory and makes a single concatenated data frame of m/z values and intensities.
1 2 | ReadMspDirectory(directory, skip = 2, comment.char = "",
remove.placeholders = TRUE)
|
directory |
character string. The path to the directory
containing the |
skip |
integer. The number of lines at the top of the input file to skip before reading. Passed internally to read.table. |
comment.char |
a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether. Passed internally to read.table. |
remove.placeholders |
TRUE or FALSE specifying if zero intensity peaks in the MSP file should be removed from the resulting data frame. |
MSP is a National Institute of Standards and Technology (NIST) text format for centroid spectra. This format is exported by some instrument software.
The spectral files do not need to have the extension .msp
. But an attempt will be made to process all files in the directory, regardless of the extension. The presense of other file types may cause errors.
ReadMspDirectory
is a wrapper for ReadMspFile
.
A data frame with the following column names:
mz |
the centroid m/z values. |
intensity |
the respective intensities. |
filename |
the corresponding filename (used to identify the spectra within the data frame). |
Nathan G. Dodder
1 2 3 | ## The package directory msp contains two .msp files
ReadMspDirectory(paste(system.file(package = "OrgMassSpecR"),
"/extdata/msp", sep = ""))
|
Loading required package: grid
[1] "Reading file /usr/lib/R/site-library/OrgMassSpecR/extdata/msp/pentaBDE.msp"
[1] "Reading file /usr/lib/R/site-library/OrgMassSpecR/extdata/msp/unknown.msp"
mz intensity filename
1 50 103 pentaBDE
2 51 8 pentaBDE
3 53 49 pentaBDE
4 60 19 pentaBDE
5 61 223 pentaBDE
6 62 612 pentaBDE
7 63 595 pentaBDE
8 64 33 pentaBDE
9 68 77 pentaBDE
10 72 5 pentaBDE
11 73 160 pentaBDE
12 74 999 pentaBDE
13 75 623 pentaBDE
14 76 35 pentaBDE
15 86 41 pentaBDE
16 87 84 pentaBDE
17 88 9 pentaBDE
18 89 2 pentaBDE
19 90 15 pentaBDE
20 98 9 pentaBDE
21 99 1 pentaBDE
22 100 2 pentaBDE
23 107 9 pentaBDE
24 108 62 pentaBDE
25 109 55 pentaBDE
26 110 31 pentaBDE
27 111 32 pentaBDE
28 112 11 pentaBDE
29 116 17 pentaBDE
30 117 36 pentaBDE
31 118 15 pentaBDE
32 119 29 pentaBDE
33 122 25 pentaBDE
34 123 28 pentaBDE
35 124 1 pentaBDE
36 128 12 pentaBDE
37 130 22 pentaBDE
38 131 5 pentaBDE
39 133 4 pentaBDE
40 134 11 pentaBDE
41 135 13 pentaBDE
42 136 46 pentaBDE
43 137 514 pentaBDE
44 138 60 pentaBDE
45 139 1 pentaBDE
46 140 18 pentaBDE
47 141 201 pentaBDE
48 142 81 pentaBDE
49 143 216 pentaBDE
50 144 59 pentaBDE
51 145 3 pentaBDE
52 147 18 pentaBDE
53 148 44 pentaBDE
54 149 19 pentaBDE
55 150 8 pentaBDE
56 152 21 pentaBDE
57 153 110 pentaBDE
58 154 114 pentaBDE
59 155 111 pentaBDE
60 156 94 pentaBDE
61 157 6 pentaBDE
62 161 4 pentaBDE
63 162 14 pentaBDE
64 163 8 pentaBDE
65 164 3 pentaBDE
66 165 13 pentaBDE
67 166 5 pentaBDE
68 167 1 pentaBDE
69 168 2 pentaBDE
70 169 2 pentaBDE
71 170 36 pentaBDE
72 171 11 pentaBDE
73 172 29 pentaBDE
74 173 15 pentaBDE
75 175 7 pentaBDE
76 177 1 pentaBDE
77 178 1 pentaBDE
78 180 1 pentaBDE
79 181 1 pentaBDE
80 186 2 pentaBDE
81 187 7 pentaBDE
82 188 10 pentaBDE
83 189 8 pentaBDE
84 190 4 pentaBDE
85 191 11 pentaBDE
86 192 4 pentaBDE
87 193 10 pentaBDE
88 194 3 pentaBDE
89 195 26 pentaBDE
90 196 4 pentaBDE
91 197 39 pentaBDE
92 198 3 pentaBDE
93 199 18 pentaBDE
94 200 1 pentaBDE
95 201 73 pentaBDE
96 202 214 pentaBDE
97 203 208 pentaBDE
98 204 74 pentaBDE
99 205 1 pentaBDE
100 214 1 pentaBDE
101 215 34 pentaBDE
102 216 98 pentaBDE
103 217 42 pentaBDE
104 218 96 pentaBDE
105 219 15 pentaBDE
106 220 26 pentaBDE
107 221 59 pentaBDE
108 222 58 pentaBDE
109 223 99 pentaBDE
110 224 37 pentaBDE
111 225 50 pentaBDE
112 226 4 pentaBDE
113 227 1 pentaBDE
114 228 1 pentaBDE
115 231 3 pentaBDE
116 232 29 pentaBDE
117 233 24 pentaBDE
118 234 61 pentaBDE
119 235 42 pentaBDE
120 236 32 pentaBDE
121 237 18 pentaBDE
122 238 1 pentaBDE
123 240 2 pentaBDE
124 241 4 pentaBDE
125 242 9 pentaBDE
126 243 10 pentaBDE
127 244 56 pentaBDE
128 245 12 pentaBDE
129 246 49 pentaBDE
130 247 9 pentaBDE
131 248 16 pentaBDE
132 249 16 pentaBDE
133 250 34 pentaBDE
134 251 24 pentaBDE
135 252 20 pentaBDE
136 253 11 pentaBDE
137 269 1 pentaBDE
138 270 1 pentaBDE
139 271 4 pentaBDE
140 272 2 pentaBDE
141 273 2 pentaBDE
142 274 1 pentaBDE
143 275 1 pentaBDE
144 280 1 pentaBDE
145 281 5 pentaBDE
146 282 9 pentaBDE
147 283 9 pentaBDE
148 284 3 pentaBDE
149 294 11 pentaBDE
150 295 147 pentaBDE
151 296 44 pentaBDE
152 297 249 pentaBDE
153 298 58 pentaBDE
154 299 141 pentaBDE
155 300 34 pentaBDE
156 301 81 pentaBDE
157 302 23 pentaBDE
158 303 81 pentaBDE
159 304 14 pentaBDE
160 305 26 pentaBDE
161 306 1 pentaBDE
162 311 3 pentaBDE
163 312 3 pentaBDE
164 313 8 pentaBDE
165 314 4 pentaBDE
166 315 6 pentaBDE
167 316 3 pentaBDE
168 317 2 pentaBDE
169 322 10 pentaBDE
170 323 24 pentaBDE
171 324 21 pentaBDE
172 325 44 pentaBDE
173 326 23 pentaBDE
174 327 29 pentaBDE
175 328 25 pentaBDE
176 329 24 pentaBDE
177 330 25 pentaBDE
178 331 22 pentaBDE
179 332 12 pentaBDE
180 333 9 pentaBDE
181 334 1 pentaBDE
182 350 1 pentaBDE
183 351 1 pentaBDE
184 352 1 pentaBDE
185 353 1 pentaBDE
186 354 1 pentaBDE
187 372 1 pentaBDE
188 373 2 pentaBDE
189 374 7 pentaBDE
190 375 7 pentaBDE
191 376 10 pentaBDE
192 377 7 pentaBDE
193 378 5 pentaBDE
194 379 2 pentaBDE
195 380 1 pentaBDE
196 400 2 pentaBDE
197 401 18 pentaBDE
198 402 325 pentaBDE
199 403 91 pentaBDE
200 404 743 pentaBDE
201 405 146 pentaBDE
202 406 486 pentaBDE
203 407 84 pentaBDE
204 408 94 pentaBDE
205 409 14 pentaBDE
206 410 2 pentaBDE
207 452 2 pentaBDE
208 453 1 pentaBDE
209 454 3 pentaBDE
210 455 4 pentaBDE
211 456 5 pentaBDE
212 457 6 pentaBDE
213 458 4 pentaBDE
214 459 3 pentaBDE
215 460 1 pentaBDE
216 461 1 pentaBDE
217 466 1 pentaBDE
218 478 1 pentaBDE
219 479 2 pentaBDE
220 481 4 pentaBDE
221 482 4 pentaBDE
222 483 9 pentaBDE
223 484 6 pentaBDE
224 485 10 pentaBDE
225 486 6 pentaBDE
226 487 6 pentaBDE
227 488 5 pentaBDE
228 489 2 pentaBDE
229 490 2 pentaBDE
230 496 1 pentaBDE
231 498 1 pentaBDE
232 500 1 pentaBDE
233 503 1 pentaBDE
234 504 1 pentaBDE
235 505 1 pentaBDE
236 514 1 pentaBDE
237 516 1 pentaBDE
238 519 1 pentaBDE
239 520 1 pentaBDE
240 522 1 pentaBDE
241 523 1 pentaBDE
242 524 1 pentaBDE
243 559 12 pentaBDE
244 560 81 pentaBDE
245 561 70 pentaBDE
246 562 371 pentaBDE
247 563 187 pentaBDE
248 564 633 pentaBDE
249 565 266 pentaBDE
250 566 492 pentaBDE
251 567 178 pentaBDE
252 568 171 pentaBDE
253 569 48 pentaBDE
254 570 23 pentaBDE
255 571 2 pentaBDE
256 572 1 pentaBDE
257 609 1 pentaBDE
258 610 1 pentaBDE
259 611 2 pentaBDE
260 612 2 pentaBDE
261 613 2 pentaBDE
262 614 1 pentaBDE
263 50 309 unknown
264 51 244 unknown
265 52 17 unknown
266 60 11 unknown
267 61 57 unknown
268 62 124 unknown
269 63 300 unknown
270 64 24 unknown
271 65 17 unknown
272 66 2 unknown
273 68 10 unknown
274 69 8 unknown
275 72 9 unknown
276 73 123 unknown
277 74 201 unknown
278 75 474 unknown
279 76 85 unknown
280 77 85 unknown
281 78 8 unknown
282 79 35 unknown
283 80 16 unknown
284 81 46 unknown
285 82 80 unknown
286 83 7 unknown
287 84 24 unknown
288 85 68 unknown
289 86 105 unknown
290 87 151 unknown
291 88 53 unknown
292 89 89 unknown
293 90 9 unknown
294 92 4 unknown
295 93 14 unknown
296 94 26 unknown
297 95 4 unknown
298 96 5 unknown
299 97 31 unknown
300 98 58 unknown
301 99 118 unknown
302 100 51 unknown
303 101 48 unknown
304 102 10 unknown
305 103 2 unknown
306 105 10 unknown
307 106 50 unknown
308 107 43 unknown
309 108 10 unknown
310 109 14 unknown
311 110 41 unknown
312 111 73 unknown
313 112 69 unknown
314 113 91 unknown
315 114 62 unknown
316 115 44 unknown
317 116 3 unknown
318 117 18 unknown
319 118 97 unknown
320 119 326 unknown
321 120 383 unknown
322 121 19 unknown
323 122 19 unknown
324 123 32 unknown
325 124 12 unknown
326 125 46 unknown
327 126 32 unknown
328 127 26 unknown
329 128 4 unknown
330 129 2 unknown
331 131 2 unknown
332 132 3 unknown
333 133 7 unknown
334 134 8 unknown
335 135 11 unknown
336 136 15 unknown
337 137 91 unknown
338 138 96 unknown
339 139 71 unknown
340 140 8 unknown
341 144 3 unknown
342 145 4 unknown
343 146 4 unknown
344 147 7 unknown
345 148 6 unknown
346 149 41 unknown
347 150 29 unknown
348 151 25 unknown
349 152 10 unknown
350 153 1 unknown
351 155 7 unknown
352 156 8 unknown
353 159 2 unknown
354 160 8 unknown
355 161 44 unknown
356 162 92 unknown
357 163 442 unknown
358 164 362 unknown
359 165 858 unknown
360 166 122 unknown
361 167 9 unknown
362 168 1 unknown
363 172 1 unknown
364 173 23 unknown
365 174 11 unknown
366 175 12 unknown
367 176 17 unknown
368 177 3 unknown
369 181 1 unknown
370 182 2 unknown
371 183 4 unknown
372 184 1 unknown
373 185 7 unknown
374 186 11 unknown
375 187 34 unknown
376 188 14 unknown
377 189 13 unknown
378 190 3 unknown
379 195 1 unknown
380 196 1 unknown
381 197 13 unknown
382 198 34 unknown
383 199 998 unknown
384 200 232 unknown
385 201 337 unknown
386 202 78 unknown
387 203 9 unknown
388 207 1 unknown
389 209 1 unknown
390 210 3 unknown
391 211 21 unknown
392 212 10 unknown
393 213 31 unknown
394 214 7 unknown
395 215 6 unknown
396 216 2 unknown
397 222 1 unknown
398 223 3 unknown
399 224 5 unknown
400 225 4 unknown
401 226 12 unknown
402 227 3 unknown
403 233 60 unknown
404 234 29 unknown
405 235 192 unknown
406 236 61 unknown
407 237 186 unknown
408 238 69 unknown
409 239 300 unknown
410 240 123 unknown
411 241 115 unknown
412 242 27 unknown
413 243 4 unknown
414 247 1 unknown
415 249 5 unknown
416 250 1 unknown
417 251 1 unknown
418 252 5 unknown
419 253 11 unknown
420 254 7 unknown
421 255 1 unknown
422 256 1 unknown
423 259 1 unknown
424 260 1 unknown
425 262 1 unknown
426 267 1 unknown
427 269 1 unknown
428 270 2 unknown
429 271 1 unknown
430 272 3 unknown
431 273 13 unknown
432 274 6 unknown
433 275 107 unknown
434 276 78 unknown
435 277 55 unknown
436 278 25 unknown
437 279 6 unknown
438 283 1 unknown
439 284 1 unknown
440 285 2 unknown
441 287 1 unknown
442 289 1 unknown
443 296 1 unknown
444 297 1 unknown
445 309 5 unknown
446 310 14 unknown
447 311 594 unknown
448 312 159 unknown
449 313 397 unknown
450 314 99 unknown
451 315 73 unknown
452 316 15 unknown
453 317 2 unknown
454 322 5 unknown
455 323 1 unknown
456 324 8 unknown
457 325 2 unknown
458 326 6 unknown
459 327 1 unknown
460 328 5 unknown
461 329 1 unknown
462 345 10 unknown
463 346 143 unknown
464 347 47 unknown
465 348 138 unknown
466 349 36 unknown
467 350 40 unknown
468 351 7 unknown
469 358 1 unknown
470 359 2 unknown
471 360 2 unknown
472 361 1 unknown
473 363 1 unknown
474 392 3 unknown
475 393 3 unknown
476 394 7 unknown
477 395 3 unknown
478 396 6 unknown
479 397 2 unknown
480 398 2 unknown
481 400 1 unknown
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