ReadMspFile: Read in a MSP Formatted Mass Spectrum
In OrgMassSpecR: Organic Mass Spectrometry
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Reads in a .msp file and makes a data frame of m/z values and intensities.
Usage
1
2
ReadMspFile(file, skip = 2, comment.char = "",
remove.placeholders = TRUE)
Arguments
file
character string. The .msp filename. Include the path to the filename if necessary.
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.
Details
MSP is a National Institute of Standards and Technology (NIST) ASCII format for centroid spectra. This format is exported by some instrument software.
The spectral file does not need to have the extension .msp.
Value
A data frame with the following column names:
mz
the centroid m/z values.
intensity
the respective intensities.
Author(s)
Nathan G. Dodder
See Also
Examples
1
ReadMspFile(paste(system.file(package = "OrgMassSpecR"), "/extdata/msp/pentaBDE.msp", sep = ""))
Example output
Loading required package: grid
mz intensity
1 50 103
2 51 8
3 53 49
4 60 19
5 61 223
6 62 612
7 63 595
8 64 33
9 68 77
10 72 5
11 73 160
12 74 999
13 75 623
14 76 35
15 86 41
16 87 84
17 88 9
18 89 2
19 90 15
20 98 9
21 99 1
22 100 2
23 107 9
24 108 62
25 109 55
26 110 31
27 111 32
28 112 11
29 116 17
30 117 36
31 118 15
32 119 29
33 122 25
34 123 28
35 124 1
36 128 12
37 130 22
38 131 5
39 133 4
40 134 11
41 135 13
42 136 46
43 137 514
44 138 60
45 139 1
46 140 18
47 141 201
48 142 81
49 143 216
50 144 59
51 145 3
52 147 18
53 148 44
54 149 19
55 150 8
56 152 21
57 153 110
58 154 114
59 155 111
60 156 94
61 157 6
62 161 4
63 162 14
64 163 8
65 164 3
66 165 13
67 166 5
68 167 1
69 168 2
70 169 2
71 170 36
72 171 11
73 172 29
74 173 15
75 175 7
76 177 1
77 178 1
78 180 1
79 181 1
80 186 2
81 187 7
82 188 10
83 189 8
84 190 4
85 191 11
86 192 4
87 193 10
88 194 3
89 195 26
90 196 4
91 197 39
92 198 3
93 199 18
94 200 1
95 201 73
96 202 214
97 203 208
98 204 74
99 205 1
100 214 1
101 215 34
102 216 98
103 217 42
104 218 96
105 219 15
106 220 26
107 221 59
108 222 58
109 223 99
110 224 37
111 225 50
112 226 4
113 227 1
114 228 1
115 231 3
116 232 29
117 233 24
118 234 61
119 235 42
120 236 32
121 237 18
122 238 1
123 240 2
124 241 4
125 242 9
126 243 10
127 244 56
128 245 12
129 246 49
130 247 9
131 248 16
132 249 16
133 250 34
134 251 24
135 252 20
136 253 11
137 269 1
138 270 1
139 271 4
140 272 2
141 273 2
142 274 1
143 275 1
144 280 1
145 281 5
146 282 9
147 283 9
148 284 3
149 294 11
150 295 147
151 296 44
152 297 249
153 298 58
154 299 141
155 300 34
156 301 81
157 302 23
158 303 81
159 304 14
160 305 26
161 306 1
162 311 3
163 312 3
164 313 8
165 314 4
166 315 6
167 316 3
168 317 2
169 322 10
170 323 24
171 324 21
172 325 44
173 326 23
174 327 29
175 328 25
176 329 24
177 330 25
178 331 22
179 332 12
180 333 9
181 334 1
182 350 1
183 351 1
184 352 1
185 353 1
186 354 1
187 372 1
188 373 2
189 374 7
190 375 7
191 376 10
192 377 7
193 378 5
194 379 2
195 380 1
196 400 2
197 401 18
198 402 325
199 403 91
200 404 743
201 405 146
202 406 486
203 407 84
204 408 94
205 409 14
206 410 2
207 452 2
208 453 1
209 454 3
210 455 4
211 456 5
212 457 6
213 458 4
214 459 3
215 460 1
216 461 1
217 466 1
218 478 1
219 479 2
220 481 4
221 482 4
222 483 9
223 484 6
224 485 10
225 486 6
226 487 6
227 488 5
228 489 2
229 490 2
230 496 1
231 498 1
232 500 1
233 503 1
234 504 1
235 505 1
236 514 1
237 516 1
238 519 1
239 520 1
240 522 1
241 523 1
242 524 1
243 559 12
244 560 81
245 561 70
246 562 371
247 563 187
248 564 633
249 565 266
250 566 492
251 567 178
252 568 171
253 569 48
254 570 23
255 571 2
256 572 1
257 609 1
258 610 1
259 611 2
260 612 2
261 613 2
262 614 1
OrgMassSpecR documentation built on May 2, 2019, 11:04 a.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Reads in a .msp file and makes a data frame of m/z values and intensities.
Usage
1 2 | ReadMspFile(file, skip = 2, comment.char = "",
remove.placeholders = TRUE)
|
Arguments
file |
character string. 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. |
Details
MSP is a National Institute of Standards and Technology (NIST) ASCII format for centroid spectra. This format is exported by some instrument software.
The spectral file does not need to have the extension .msp.
Value
A data frame with the following column names:
mz |
the centroid m/z values. |
intensity |
the respective intensities. |
Author(s)
Nathan G. Dodder
See Also
Examples
1 | ReadMspFile(paste(system.file(package = "OrgMassSpecR"), "/extdata/msp/pentaBDE.msp", sep = ""))
|
Example output
Loading required package: grid
mz intensity
1 50 103
2 51 8
3 53 49
4 60 19
5 61 223
6 62 612
7 63 595
8 64 33
9 68 77
10 72 5
11 73 160
12 74 999
13 75 623
14 76 35
15 86 41
16 87 84
17 88 9
18 89 2
19 90 15
20 98 9
21 99 1
22 100 2
23 107 9
24 108 62
25 109 55
26 110 31
27 111 32
28 112 11
29 116 17
30 117 36
31 118 15
32 119 29
33 122 25
34 123 28
35 124 1
36 128 12
37 130 22
38 131 5
39 133 4
40 134 11
41 135 13
42 136 46
43 137 514
44 138 60
45 139 1
46 140 18
47 141 201
48 142 81
49 143 216
50 144 59
51 145 3
52 147 18
53 148 44
54 149 19
55 150 8
56 152 21
57 153 110
58 154 114
59 155 111
60 156 94
61 157 6
62 161 4
63 162 14
64 163 8
65 164 3
66 165 13
67 166 5
68 167 1
69 168 2
70 169 2
71 170 36
72 171 11
73 172 29
74 173 15
75 175 7
76 177 1
77 178 1
78 180 1
79 181 1
80 186 2
81 187 7
82 188 10
83 189 8
84 190 4
85 191 11
86 192 4
87 193 10
88 194 3
89 195 26
90 196 4
91 197 39
92 198 3
93 199 18
94 200 1
95 201 73
96 202 214
97 203 208
98 204 74
99 205 1
100 214 1
101 215 34
102 216 98
103 217 42
104 218 96
105 219 15
106 220 26
107 221 59
108 222 58
109 223 99
110 224 37
111 225 50
112 226 4
113 227 1
114 228 1
115 231 3
116 232 29
117 233 24
118 234 61
119 235 42
120 236 32
121 237 18
122 238 1
123 240 2
124 241 4
125 242 9
126 243 10
127 244 56
128 245 12
129 246 49
130 247 9
131 248 16
132 249 16
133 250 34
134 251 24
135 252 20
136 253 11
137 269 1
138 270 1
139 271 4
140 272 2
141 273 2
142 274 1
143 275 1
144 280 1
145 281 5
146 282 9
147 283 9
148 284 3
149 294 11
150 295 147
151 296 44
152 297 249
153 298 58
154 299 141
155 300 34
156 301 81
157 302 23
158 303 81
159 304 14
160 305 26
161 306 1
162 311 3
163 312 3
164 313 8
165 314 4
166 315 6
167 316 3
168 317 2
169 322 10
170 323 24
171 324 21
172 325 44
173 326 23
174 327 29
175 328 25
176 329 24
177 330 25
178 331 22
179 332 12
180 333 9
181 334 1
182 350 1
183 351 1
184 352 1
185 353 1
186 354 1
187 372 1
188 373 2
189 374 7
190 375 7
191 376 10
192 377 7
193 378 5
194 379 2
195 380 1
196 400 2
197 401 18
198 402 325
199 403 91
200 404 743
201 405 146
202 406 486
203 407 84
204 408 94
205 409 14
206 410 2
207 452 2
208 453 1
209 454 3
210 455 4
211 456 5
212 457 6
213 458 4
214 459 3
215 460 1
216 461 1
217 466 1
218 478 1
219 479 2
220 481 4
221 482 4
222 483 9
223 484 6
224 485 10
225 486 6
226 487 6
227 488 5
228 489 2
229 490 2
230 496 1
231 498 1
232 500 1
233 503 1
234 504 1
235 505 1
236 514 1
237 516 1
238 519 1
239 520 1
240 522 1
241 523 1
242 524 1
243 559 12
244 560 81
245 561 70
246 562 371
247 563 187
248 564 633
249 565 266
250 566 492
251 567 178
252 568 171
253 569 48
254 570 23
255 571 2
256 572 1
257 609 1
258 610 1
259 611 2
260 612 2
261 613 2
262 614 1
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