getfreqs: Get frequencies for amino acids/nucleotides in alignment...
In SeqFeatR: A Tool to Associate FASTA Sequences and Features
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Gets frequencies of amino acids/nucleotides inside an epitope out of an alignment. Epitope start and end positions must be in the range of the length of the alignment, starting with the first position of the alignment as one. You can add the whole sequence consensus, but also a part of it.
Usage
1
2
3
4
Arguments
path_to_file_sequence_alignment
a FASTA file with sequence data. For reference please look in example file.
save_csv
name for the csv output.
save_png
name for the png/svg output.
epitope_position_start
starting position of the epitope in the alignment.
epitope_position_end
ending position of the epitope in the alignment.
path_to_file_consensus
a FASTA file with the consensus sequence from epi_pos_start till epi_pos_end.
patnum_threshold
the minimum number of patients of one HLA type to consider in the calculation.
A11
the position of the start of the first HLA A allele in the description block of the FASTA file.
A12
the position of the end of the first HLA A allele in the description block of the FASTA file.
A21
the position of the start of the second HLA A allele in the description block of the FASTA file.
A22
the position of the end of the second HLA A allele in the description block of the FASTA file.
B11
the position of the start of the first HLA B allele in the description block of the FASTA file.
B12
the position of the end of the first HLA B allele in the description block of the FASTA file.
B21
the position of the start of the second HLA B allele in the description block of the FASTA file.
B22
the position of the end of the second HLA B allele in the description block of the FASTA file.
one_feature
if there is only one feature.
Details
This function counts the number of amino acids NOT being the same as the consensus
and generates an output graphic as well as a result csv file.
The features may be HLA types, indicated by four blocks in the FASTA
comment lines. The positions of these blocks in the comment lines are
defined by parameters A11, ..., B22. For patients with a homozygous
HLA allele the second allele has to be "00" (without the double
quotes). For non-HLA-type features, set option one_feature=TRUE. The
value of the feature (e.g. 'yes / no', or '1 / 2 / 3') should then be
given at the end of each FASTA comment, separated from the part before
that by a semicolon.
Value
A csv file with a row for each feature and two columns (absolute and relative) for the frequencies of the amino acids in the epitope.
Author(s)
Bettina Budeus
See Also
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
#Input files
fasta_input <- system.file("extdata", "Example_aa.fasta", package="SeqFeatR")
consensus_input <- system.file("extdata", "Example_Consensus_aa.fasta", package="SeqFeatR")
#Usage
getfreqs(
path_to_file_sequence_alignment=fasta_input,
save_csv="getfreqs_result.csv",
save_png="getfreqs_result.png",
epitope_position_start=1,
epitope_position_end=40,
path_to_file_consensus=consensus_input,
patnum_threshold=1,
A11=10,
A12=11,
A21=13,
A22=14,
B11=17,
B12=18,
B21=20,
B22=21,
one_feature=FALSE)
Example output
Loading required package: tcltk
Loading required package: tcltk2
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:tcltk2’:
values, values<-
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: plotrix
Warning message:
no DISPLAY variable so Tk is not available
allel: 1
allel: 2
allel: 3
allel: 4
allel: 5
allel: 6
allel: 7
allel: 8
Allels letter I_abs kind
1 A1 1_I 6 allel
2 A1 2_P 1 allel
3 A1 3_D 0 allel
4 A1 4_T 6 allel
5 A1 5_N 6 allel
6 A1 6_G 4 allel
7 A1 7_C 7 allel
8 A1 8_T 6 allel
9 A1 9_C 5 allel
10 A1 10_G 7 allel
11 A1 11_I 6 allel
12 A1 12_Q 7 allel
13 A1 13_Q 5 allel
14 A1 14_A 5 allel
15 A1 15_L 5 allel
16 A1 16_I 5 allel
17 A1 17_W 7 allel
18 A1 18_W 7 allel
19 A1 19_G 6 allel
20 A1 20_G 5 allel
21 A1 21_H 6 allel
22 A1 22_E 6 allel
23 A1 23_H 5 allel
24 A1 24_M 7 allel
25 A1 25_I 6 allel
26 A1 26_K 7 allel
27 A1 27_Q 0 allel
28 A1 28_L 5 allel
29 A1 29_L 5 allel
30 A1 30_C 6 allel
31 A1 31_I 6 allel
32 A1 32_V 5 allel
33 A1 33_H 5 allel
34 A1 34_I 6 allel
35 A1 35_C 6 allel
36 A1 36_G 6 allel
37 A1 37_E 7 allel
38 A1 38_C 7 allel
39 A1 39_N 5 allel
40 A1 40_W 5 allel
41 A2 1_I 2 allel
42 A2 2_P 1 allel
43 A2 3_D 0 allel
44 A2 4_T 3 allel
45 A2 5_N 3 allel
46 A2 6_G 2 allel
47 A2 7_C 3 allel
48 A2 8_T 3 allel
49 A2 9_C 2 allel
50 A2 10_G 3 allel
51 A2 11_I 2 allel
52 A2 12_Q 3 allel
53 A2 13_Q 2 allel
54 A2 14_A 3 allel
55 A2 15_L 2 allel
56 A2 16_I 3 allel
57 A2 17_W 3 allel
58 A2 18_W 3 allel
59 A2 19_G 3 allel
60 A2 20_G 2 allel
61 A2 21_H 3 allel
62 A2 22_E 3 allel
63 A2 23_H 1 allel
64 A2 24_M 3 allel
65 A2 25_I 3 allel
66 A2 26_K 3 allel
67 A2 27_Q 0 allel
68 A2 28_L 1 allel
69 A2 29_L 3 allel
70 A2 30_C 3 allel
71 A2 31_I 2 allel
72 A2 32_V 3 allel
73 A2 33_H 3 allel
74 A2 34_I 3 allel
75 A2 35_C 3 allel
76 A2 36_G 2 allel
77 A2 37_E 3 allel
78 A2 38_C 3 allel
79 A2 39_N 3 allel
80 A2 40_W 2 allel
81 A3 1_I 6 allel
82 A3 2_P 6 allel
83 A3 3_D 7 allel
84 A3 4_T 0 allel
85 A3 5_N 6 allel
86 A3 6_G 6 allel
87 A3 7_C 5 allel
88 A3 8_T 5 allel
89 A3 9_C 5 allel
90 A3 10_G 5 allel
91 A3 11_I 5 allel
92 A3 12_Q 4 allel
93 A3 13_Q 6 allel
94 A3 14_A 7 allel
95 A3 15_L 5 allel
96 A3 16_I 6 allel
97 A3 17_W 4 allel
98 A3 18_W 5 allel
99 A3 19_G 5 allel
100 A3 20_G 7 allel
101 A3 21_H 6 allel
102 A3 22_E 6 allel
103 A3 23_H 5 allel
104 A3 24_M 5 allel
105 A3 25_I 5 allel
106 A3 26_K 4 allel
107 A3 27_Q 7 allel
108 A3 28_L 5 allel
109 A3 29_L 6 allel
110 A3 30_C 6 allel
111 A3 31_I 5 allel
112 A3 32_V 7 allel
113 A3 33_H 6 allel
114 A3 34_I 5 allel
115 A3 35_C 5 allel
116 A3 36_G 5 allel
117 A3 37_E 5 allel
118 A3 38_C 5 allel
119 A3 39_N 6 allel
120 A3 40_W 6 allel
121 A4 1_I 6 allel
122 A4 2_P 6 allel
123 A4 3_D 7 allel
124 A4 4_T 0 allel
125 A4 5_N 6 allel
126 A4 6_G 6 allel
127 A4 7_C 5 allel
128 A4 8_T 5 allel
129 A4 9_C 5 allel
130 A4 10_G 5 allel
131 A4 11_I 5 allel
132 A4 12_Q 4 allel
133 A4 13_Q 6 allel
134 A4 14_A 7 allel
135 A4 15_L 5 allel
136 A4 16_I 6 allel
137 A4 17_W 4 allel
138 A4 18_W 5 allel
139 A4 19_G 5 allel
140 A4 20_G 7 allel
141 A4 21_H 6 allel
142 A4 22_E 6 allel
143 A4 23_H 5 allel
144 A4 24_M 5 allel
145 A4 25_I 5 allel
146 A4 26_K 4 allel
147 A4 27_Q 7 allel
148 A4 28_L 5 allel
149 A4 29_L 6 allel
150 A4 30_C 6 allel
151 A4 31_I 5 allel
152 A4 32_V 7 allel
153 A4 33_H 6 allel
154 A4 34_I 5 allel
155 A4 35_C 5 allel
156 A4 36_G 5 allel
157 A4 37_E 5 allel
158 A4 38_C 5 allel
159 A4 39_N 6 allel
160 A4 40_W 6 allel
161 B1 1_I 6 allel
162 B1 2_P 1 allel
163 B1 3_D 0 allel
164 B1 4_T 6 allel
165 B1 5_N 6 allel
166 B1 6_G 4 allel
167 B1 7_C 7 allel
168 B1 8_T 6 allel
169 B1 9_C 5 allel
170 B1 10_G 7 allel
171 B1 11_I 6 allel
172 B1 12_Q 7 allel
173 B1 13_Q 5 allel
174 B1 14_A 5 allel
175 B1 15_L 5 allel
176 B1 16_I 5 allel
177 B1 17_W 7 allel
178 B1 18_W 7 allel
179 B1 19_G 6 allel
180 B1 20_G 5 allel
181 B1 21_H 6 allel
182 B1 22_E 6 allel
183 B1 23_H 5 allel
184 B1 24_M 7 allel
185 B1 25_I 6 allel
186 B1 26_K 7 allel
187 B1 27_Q 0 allel
188 B1 28_L 5 allel
189 B1 29_L 5 allel
190 B1 30_C 6 allel
191 B1 31_I 6 allel
192 B1 32_V 5 allel
193 B1 33_H 5 allel
194 B1 34_I 6 allel
195 B1 35_C 6 allel
196 B1 36_G 6 allel
197 B1 37_E 7 allel
198 B1 38_C 7 allel
199 B1 39_N 5 allel
200 B1 40_W 5 allel
201 B2 1_I 6 allel
202 B2 2_P 1 allel
203 B2 3_D 0 allel
204 B2 4_T 6 allel
205 B2 5_N 6 allel
206 B2 6_G 4 allel
207 B2 7_C 7 allel
208 B2 8_T 6 allel
209 B2 9_C 5 allel
210 B2 10_G 7 allel
211 B2 11_I 6 allel
212 B2 12_Q 7 allel
213 B2 13_Q 5 allel
214 B2 14_A 5 allel
215 B2 15_L 5 allel
216 B2 16_I 5 allel
217 B2 17_W 7 allel
218 B2 18_W 7 allel
219 B2 19_G 6 allel
220 B2 20_G 5 allel
221 B2 21_H 6 allel
222 B2 22_E 6 allel
223 B2 23_H 5 allel
224 B2 24_M 7 allel
225 B2 25_I 6 allel
226 B2 26_K 7 allel
227 B2 27_Q 0 allel
228 B2 28_L 5 allel
229 B2 29_L 5 allel
230 B2 30_C 6 allel
231 B2 31_I 6 allel
232 B2 32_V 5 allel
233 B2 33_H 5 allel
234 B2 34_I 6 allel
235 B2 35_C 6 allel
236 B2 36_G 6 allel
237 B2 37_E 7 allel
238 B2 38_C 7 allel
239 B2 39_N 5 allel
240 B2 40_W 5 allel
241 B3 1_I 5 allel
242 B3 2_P 4 allel
243 B3 3_D 5 allel
244 B3 4_T 0 allel
245 B3 5_N 4 allel
246 B3 6_G 4 allel
247 B3 7_C 4 allel
248 B3 8_T 3 allel
249 B3 9_C 5 allel
250 B3 10_G 3 allel
251 B3 11_I 4 allel
252 B3 12_Q 2 allel
253 B3 13_Q 5 allel
254 B3 14_A 5 allel
255 B3 15_L 3 allel
256 B3 16_I 5 allel
257 B3 17_W 3 allel
258 B3 18_W 5 allel
259 B3 19_G 3 allel
260 B3 20_G 5 allel
261 B3 21_H 5 allel
262 B3 22_E 4 allel
263 B3 23_H 4 allel
264 B3 24_M 4 allel
265 B3 25_I 4 allel
266 B3 26_K 2 allel
267 B3 27_Q 5 allel
268 B3 28_L 3 allel
269 B3 29_L 4 allel
270 B3 30_C 4 allel
271 B3 31_I 3 allel
272 B3 32_V 5 allel
273 B3 33_H 4 allel
274 B3 34_I 3 allel
275 B3 35_C 4 allel
276 B3 36_G 3 allel
277 B3 37_E 3 allel
278 B3 38_C 3 allel
279 B3 39_N 4 allel
280 B3 40_W 4 allel
281 B4 1_I 6 allel
282 B4 2_P 6 allel
283 B4 3_D 7 allel
284 B4 4_T 0 allel
285 B4 5_N 6 allel
286 B4 6_G 6 allel
287 B4 7_C 5 allel
288 B4 8_T 5 allel
289 B4 9_C 5 allel
290 B4 10_G 5 allel
291 B4 11_I 5 allel
292 B4 12_Q 4 allel
293 B4 13_Q 6 allel
294 B4 14_A 7 allel
295 B4 15_L 5 allel
296 B4 16_I 6 allel
297 B4 17_W 4 allel
298 B4 18_W 5 allel
299 B4 19_G 5 allel
300 B4 20_G 7 allel
301 B4 21_H 6 allel
302 B4 22_E 6 allel
303 B4 23_H 5 allel
304 B4 24_M 5 allel
305 B4 25_I 5 allel
306 B4 26_K 4 allel
307 B4 27_Q 7 allel
308 B4 28_L 5 allel
309 B4 29_L 6 allel
310 B4 30_C 6 allel
311 B4 31_I 5 allel
312 B4 32_V 7 allel
313 B4 33_H 6 allel
314 B4 34_I 5 allel
315 B4 35_C 5 allel
316 B4 36_G 5 allel
317 B4 37_E 5 allel
318 B4 38_C 5 allel
319 B4 39_N 6 allel
320 B4 40_W 6 allel
321 A1 1_I 6 not allel
322 A1 2_P 6 not allel
323 A1 3_D 7 not allel
324 A1 4_T 0 not allel
325 A1 5_N 6 not allel
326 A1 6_G 6 not allel
327 A1 7_C 5 not allel
328 A1 8_T 5 not allel
329 A1 9_C 5 not allel
330 A1 10_G 5 not allel
331 A1 11_I 5 not allel
332 A1 12_Q 4 not allel
333 A1 13_Q 6 not allel
334 A1 14_A 7 not allel
335 A1 15_L 5 not allel
336 A1 16_I 6 not allel
337 A1 17_W 4 not allel
338 A1 18_W 5 not allel
339 A1 19_G 5 not allel
340 A1 20_G 7 not allel
341 A1 21_H 6 not allel
342 A1 22_E 6 not allel
343 A1 23_H 5 not allel
344 A1 24_M 5 not allel
345 A1 25_I 5 not allel
346 A1 26_K 4 not allel
347 A1 27_Q 7 not allel
348 A1 28_L 5 not allel
349 A1 29_L 6 not allel
350 A1 30_C 6 not allel
351 A1 31_I 5 not allel
352 A1 32_V 7 not allel
353 A1 33_H 6 not allel
354 A1 34_I 5 not allel
355 A1 35_C 5 not allel
356 A1 36_G 5 not allel
357 A1 37_E 5 not allel
358 A1 38_C 5 not allel
359 A1 39_N 6 not allel
360 A1 40_W 6 not allel
361 A2 1_I 10 not allel
362 A2 2_P 6 not allel
363 A2 3_D 7 not allel
364 A2 4_T 3 not allel
365 A2 5_N 9 not allel
366 A2 6_G 8 not allel
367 A2 7_C 9 not allel
368 A2 8_T 8 not allel
369 A2 9_C 8 not allel
370 A2 10_G 9 not allel
371 A2 11_I 9 not allel
372 A2 12_Q 8 not allel
373 A2 13_Q 9 not allel
374 A2 14_A 9 not allel
375 A2 15_L 8 not allel
376 A2 16_I 8 not allel
377 A2 17_W 8 not allel
378 A2 18_W 9 not allel
379 A2 19_G 8 not allel
380 A2 20_G 10 not allel
381 A2 21_H 9 not allel
382 A2 22_E 9 not allel
383 A2 23_H 9 not allel
384 A2 24_M 9 not allel
385 A2 25_I 8 not allel
386 A2 26_K 8 not allel
387 A2 27_Q 7 not allel
388 A2 28_L 9 not allel
389 A2 29_L 8 not allel
390 A2 30_C 9 not allel
391 A2 31_I 9 not allel
392 A2 32_V 9 not allel
393 A2 33_H 8 not allel
394 A2 34_I 8 not allel
395 A2 35_C 8 not allel
396 A2 36_G 9 not allel
397 A2 37_E 9 not allel
398 A2 38_C 9 not allel
399 A2 39_N 8 not allel
400 A2 40_W 9 not allel
401 A3 1_I 6 not allel
402 A3 2_P 1 not allel
403 A3 3_D 0 not allel
404 A3 4_T 6 not allel
405 A3 5_N 6 not allel
406 A3 6_G 4 not allel
407 A3 7_C 7 not allel
408 A3 8_T 6 not allel
409 A3 9_C 5 not allel
410 A3 10_G 7 not allel
411 A3 11_I 6 not allel
412 A3 12_Q 7 not allel
413 A3 13_Q 5 not allel
414 A3 14_A 5 not allel
415 A3 15_L 5 not allel
416 A3 16_I 5 not allel
417 A3 17_W 7 not allel
418 A3 18_W 7 not allel
419 A3 19_G 6 not allel
420 A3 20_G 5 not allel
421 A3 21_H 6 not allel
422 A3 22_E 6 not allel
423 A3 23_H 5 not allel
424 A3 24_M 7 not allel
425 A3 25_I 6 not allel
426 A3 26_K 7 not allel
427 A3 27_Q 0 not allel
428 A3 28_L 5 not allel
429 A3 29_L 5 not allel
430 A3 30_C 6 not allel
431 A3 31_I 6 not allel
432 A3 32_V 5 not allel
433 A3 33_H 5 not allel
434 A3 34_I 6 not allel
435 A3 35_C 6 not allel
436 A3 36_G 6 not allel
437 A3 37_E 7 not allel
438 A3 38_C 7 not allel
439 A3 39_N 5 not allel
440 A3 40_W 5 not allel
441 A4 1_I 6 not allel
442 A4 2_P 1 not allel
443 A4 3_D 0 not allel
444 A4 4_T 6 not allel
445 A4 5_N 6 not allel
446 A4 6_G 4 not allel
447 A4 7_C 7 not allel
448 A4 8_T 6 not allel
449 A4 9_C 5 not allel
450 A4 10_G 7 not allel
451 A4 11_I 6 not allel
452 A4 12_Q 7 not allel
453 A4 13_Q 5 not allel
454 A4 14_A 5 not allel
455 A4 15_L 5 not allel
456 A4 16_I 5 not allel
457 A4 17_W 7 not allel
458 A4 18_W 7 not allel
459 A4 19_G 6 not allel
460 A4 20_G 5 not allel
461 A4 21_H 6 not allel
462 A4 22_E 6 not allel
463 A4 23_H 5 not allel
464 A4 24_M 7 not allel
465 A4 25_I 6 not allel
466 A4 26_K 7 not allel
467 A4 27_Q 0 not allel
468 A4 28_L 5 not allel
469 A4 29_L 5 not allel
470 A4 30_C 6 not allel
471 A4 31_I 6 not allel
472 A4 32_V 5 not allel
473 A4 33_H 5 not allel
474 A4 34_I 6 not allel
475 A4 35_C 6 not allel
476 A4 36_G 6 not allel
477 A4 37_E 7 not allel
478 A4 38_C 7 not allel
479 A4 39_N 5 not allel
480 A4 40_W 5 not allel
481 B1 1_I 6 not allel
482 B1 2_P 6 not allel
483 B1 3_D 7 not allel
484 B1 4_T 0 not allel
485 B1 5_N 6 not allel
486 B1 6_G 6 not allel
487 B1 7_C 5 not allel
488 B1 8_T 5 not allel
489 B1 9_C 5 not allel
490 B1 10_G 5 not allel
491 B1 11_I 5 not allel
492 B1 12_Q 4 not allel
493 B1 13_Q 6 not allel
494 B1 14_A 7 not allel
495 B1 15_L 5 not allel
496 B1 16_I 6 not allel
497 B1 17_W 4 not allel
498 B1 18_W 5 not allel
499 B1 19_G 5 not allel
500 B1 20_G 7 not allel
501 B1 21_H 6 not allel
502 B1 22_E 6 not allel
503 B1 23_H 5 not allel
504 B1 24_M 5 not allel
505 B1 25_I 5 not allel
506 B1 26_K 4 not allel
507 B1 27_Q 7 not allel
508 B1 28_L 5 not allel
509 B1 29_L 6 not allel
510 B1 30_C 6 not allel
511 B1 31_I 5 not allel
512 B1 32_V 7 not allel
513 B1 33_H 6 not allel
514 B1 34_I 5 not allel
515 B1 35_C 5 not allel
516 B1 36_G 5 not allel
517 B1 37_E 5 not allel
518 B1 38_C 5 not allel
519 B1 39_N 6 not allel
520 B1 40_W 6 not allel
521 B2 1_I 6 not allel
522 B2 2_P 6 not allel
523 B2 3_D 7 not allel
524 B2 4_T 0 not allel
525 B2 5_N 6 not allel
526 B2 6_G 6 not allel
527 B2 7_C 5 not allel
528 B2 8_T 5 not allel
529 B2 9_C 5 not allel
530 B2 10_G 5 not allel
531 B2 11_I 5 not allel
532 B2 12_Q 4 not allel
533 B2 13_Q 6 not allel
534 B2 14_A 7 not allel
535 B2 15_L 5 not allel
536 B2 16_I 6 not allel
537 B2 17_W 4 not allel
538 B2 18_W 5 not allel
539 B2 19_G 5 not allel
540 B2 20_G 7 not allel
541 B2 21_H 6 not allel
542 B2 22_E 6 not allel
543 B2 23_H 5 not allel
544 B2 24_M 5 not allel
545 B2 25_I 5 not allel
546 B2 26_K 4 not allel
547 B2 27_Q 7 not allel
548 B2 28_L 5 not allel
549 B2 29_L 6 not allel
550 B2 30_C 6 not allel
551 B2 31_I 5 not allel
552 B2 32_V 7 not allel
553 B2 33_H 6 not allel
554 B2 34_I 5 not allel
555 B2 35_C 5 not allel
556 B2 36_G 5 not allel
557 B2 37_E 5 not allel
558 B2 38_C 5 not allel
559 B2 39_N 6 not allel
560 B2 40_W 6 not allel
561 B3 1_I 7 not allel
562 B3 2_P 3 not allel
563 B3 3_D 2 not allel
564 B3 4_T 6 not allel
565 B3 5_N 8 not allel
566 B3 6_G 6 not allel
567 B3 7_C 8 not allel
568 B3 8_T 8 not allel
569 B3 9_C 5 not allel
570 B3 10_G 9 not allel
571 B3 11_I 7 not allel
572 B3 12_Q 9 not allel
573 B3 13_Q 6 not allel
574 B3 14_A 7 not allel
575 B3 15_L 7 not allel
576 B3 16_I 6 not allel
577 B3 17_W 8 not allel
578 B3 18_W 7 not allel
579 B3 19_G 8 not allel
580 B3 20_G 7 not allel
581 B3 21_H 7 not allel
582 B3 22_E 8 not allel
583 B3 23_H 6 not allel
584 B3 24_M 8 not allel
585 B3 25_I 7 not allel
586 B3 26_K 9 not allel
587 B3 27_Q 2 not allel
588 B3 28_L 7 not allel
589 B3 29_L 7 not allel
590 B3 30_C 8 not allel
591 B3 31_I 8 not allel
592 B3 32_V 7 not allel
593 B3 33_H 7 not allel
594 B3 34_I 8 not allel
595 B3 35_C 7 not allel
596 B3 36_G 8 not allel
597 B3 37_E 9 not allel
598 B3 38_C 9 not allel
599 B3 39_N 7 not allel
600 B3 40_W 7 not allel
601 B4 1_I 6 not allel
602 B4 2_P 1 not allel
603 B4 3_D 0 not allel
604 B4 4_T 6 not allel
605 B4 5_N 6 not allel
606 B4 6_G 4 not allel
607 B4 7_C 7 not allel
608 B4 8_T 6 not allel
609 B4 9_C 5 not allel
610 B4 10_G 7 not allel
611 B4 11_I 6 not allel
612 B4 12_Q 7 not allel
613 B4 13_Q 5 not allel
614 B4 14_A 5 not allel
615 B4 15_L 5 not allel
616 B4 16_I 5 not allel
617 B4 17_W 7 not allel
618 B4 18_W 7 not allel
619 B4 19_G 6 not allel
620 B4 20_G 5 not allel
621 B4 21_H 6 not allel
622 B4 22_E 6 not allel
623 B4 23_H 5 not allel
624 B4 24_M 7 not allel
625 B4 25_I 6 not allel
626 B4 26_K 7 not allel
627 B4 27_Q 0 not allel
628 B4 28_L 5 not allel
629 B4 29_L 5 not allel
630 B4 30_C 6 not allel
631 B4 31_I 6 not allel
632 B4 32_V 5 not allel
633 B4 33_H 5 not allel
634 B4 34_I 6 not allel
635 B4 35_C 6 not allel
636 B4 36_G 6 not allel
637 B4 37_E 7 not allel
638 B4 38_C 7 not allel
639 B4 39_N 5 not allel
640 B4 40_W 5 not allel
Saving 6.67 x 6.67 in image
SeqFeatR documentation built on May 2, 2019, 3:10 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) See Also Examples
Description
Gets frequencies of amino acids/nucleotides inside an epitope out of an alignment. Epitope start and end positions must be in the range of the length of the alignment, starting with the first position of the alignment as one. You can add the whole sequence consensus, but also a part of it.
Usage
1 2 3 4 |
Arguments
path_to_file_sequence_alignment |
a FASTA file with sequence data. For reference please look in example file. |
save_csv |
name for the csv output. |
save_png |
name for the png/svg output. |
epitope_position_start |
starting position of the epitope in the alignment. |
epitope_position_end |
ending position of the epitope in the alignment. |
path_to_file_consensus |
a FASTA file with the consensus sequence from epi_pos_start till epi_pos_end. |
patnum_threshold |
the minimum number of patients of one HLA type to consider in the calculation. |
A11 |
the position of the start of the first HLA A allele in the description block of the FASTA file. |
A12 |
the position of the end of the first HLA A allele in the description block of the FASTA file. |
A21 |
the position of the start of the second HLA A allele in the description block of the FASTA file. |
A22 |
the position of the end of the second HLA A allele in the description block of the FASTA file. |
B11 |
the position of the start of the first HLA B allele in the description block of the FASTA file. |
B12 |
the position of the end of the first HLA B allele in the description block of the FASTA file. |
B21 |
the position of the start of the second HLA B allele in the description block of the FASTA file. |
B22 |
the position of the end of the second HLA B allele in the description block of the FASTA file. |
one_feature |
if there is only one feature. |
Details
This function counts the number of amino acids NOT being the same as the consensus and generates an output graphic as well as a result csv file.
The features may be HLA types, indicated by four blocks in the FASTA comment lines. The positions of these blocks in the comment lines are defined by parameters A11, ..., B22. For patients with a homozygous HLA allele the second allele has to be "00" (without the double quotes). For non-HLA-type features, set option one_feature=TRUE. The value of the feature (e.g. 'yes / no', or '1 / 2 / 3') should then be given at the end of each FASTA comment, separated from the part before that by a semicolon.
Value
A csv file with a row for each feature and two columns (absolute and relative) for the frequencies of the amino acids in the epitope.
Author(s)
Bettina Budeus
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | #Input files
fasta_input <- system.file("extdata", "Example_aa.fasta", package="SeqFeatR")
consensus_input <- system.file("extdata", "Example_Consensus_aa.fasta", package="SeqFeatR")
#Usage
getfreqs(
path_to_file_sequence_alignment=fasta_input,
save_csv="getfreqs_result.csv",
save_png="getfreqs_result.png",
epitope_position_start=1,
epitope_position_end=40,
path_to_file_consensus=consensus_input,
patnum_threshold=1,
A11=10,
A12=11,
A21=13,
A22=14,
B11=17,
B12=18,
B21=20,
B22=21,
one_feature=FALSE)
|
Example output
Loading required package: tcltk
Loading required package: tcltk2
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following objects are masked from ‘package:tcltk2’:
values, values<-
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: plotrix
Warning message:
no DISPLAY variable so Tk is not available
allel: 1
allel: 2
allel: 3
allel: 4
allel: 5
allel: 6
allel: 7
allel: 8
Allels letter I_abs kind
1 A1 1_I 6 allel
2 A1 2_P 1 allel
3 A1 3_D 0 allel
4 A1 4_T 6 allel
5 A1 5_N 6 allel
6 A1 6_G 4 allel
7 A1 7_C 7 allel
8 A1 8_T 6 allel
9 A1 9_C 5 allel
10 A1 10_G 7 allel
11 A1 11_I 6 allel
12 A1 12_Q 7 allel
13 A1 13_Q 5 allel
14 A1 14_A 5 allel
15 A1 15_L 5 allel
16 A1 16_I 5 allel
17 A1 17_W 7 allel
18 A1 18_W 7 allel
19 A1 19_G 6 allel
20 A1 20_G 5 allel
21 A1 21_H 6 allel
22 A1 22_E 6 allel
23 A1 23_H 5 allel
24 A1 24_M 7 allel
25 A1 25_I 6 allel
26 A1 26_K 7 allel
27 A1 27_Q 0 allel
28 A1 28_L 5 allel
29 A1 29_L 5 allel
30 A1 30_C 6 allel
31 A1 31_I 6 allel
32 A1 32_V 5 allel
33 A1 33_H 5 allel
34 A1 34_I 6 allel
35 A1 35_C 6 allel
36 A1 36_G 6 allel
37 A1 37_E 7 allel
38 A1 38_C 7 allel
39 A1 39_N 5 allel
40 A1 40_W 5 allel
41 A2 1_I 2 allel
42 A2 2_P 1 allel
43 A2 3_D 0 allel
44 A2 4_T 3 allel
45 A2 5_N 3 allel
46 A2 6_G 2 allel
47 A2 7_C 3 allel
48 A2 8_T 3 allel
49 A2 9_C 2 allel
50 A2 10_G 3 allel
51 A2 11_I 2 allel
52 A2 12_Q 3 allel
53 A2 13_Q 2 allel
54 A2 14_A 3 allel
55 A2 15_L 2 allel
56 A2 16_I 3 allel
57 A2 17_W 3 allel
58 A2 18_W 3 allel
59 A2 19_G 3 allel
60 A2 20_G 2 allel
61 A2 21_H 3 allel
62 A2 22_E 3 allel
63 A2 23_H 1 allel
64 A2 24_M 3 allel
65 A2 25_I 3 allel
66 A2 26_K 3 allel
67 A2 27_Q 0 allel
68 A2 28_L 1 allel
69 A2 29_L 3 allel
70 A2 30_C 3 allel
71 A2 31_I 2 allel
72 A2 32_V 3 allel
73 A2 33_H 3 allel
74 A2 34_I 3 allel
75 A2 35_C 3 allel
76 A2 36_G 2 allel
77 A2 37_E 3 allel
78 A2 38_C 3 allel
79 A2 39_N 3 allel
80 A2 40_W 2 allel
81 A3 1_I 6 allel
82 A3 2_P 6 allel
83 A3 3_D 7 allel
84 A3 4_T 0 allel
85 A3 5_N 6 allel
86 A3 6_G 6 allel
87 A3 7_C 5 allel
88 A3 8_T 5 allel
89 A3 9_C 5 allel
90 A3 10_G 5 allel
91 A3 11_I 5 allel
92 A3 12_Q 4 allel
93 A3 13_Q 6 allel
94 A3 14_A 7 allel
95 A3 15_L 5 allel
96 A3 16_I 6 allel
97 A3 17_W 4 allel
98 A3 18_W 5 allel
99 A3 19_G 5 allel
100 A3 20_G 7 allel
101 A3 21_H 6 allel
102 A3 22_E 6 allel
103 A3 23_H 5 allel
104 A3 24_M 5 allel
105 A3 25_I 5 allel
106 A3 26_K 4 allel
107 A3 27_Q 7 allel
108 A3 28_L 5 allel
109 A3 29_L 6 allel
110 A3 30_C 6 allel
111 A3 31_I 5 allel
112 A3 32_V 7 allel
113 A3 33_H 6 allel
114 A3 34_I 5 allel
115 A3 35_C 5 allel
116 A3 36_G 5 allel
117 A3 37_E 5 allel
118 A3 38_C 5 allel
119 A3 39_N 6 allel
120 A3 40_W 6 allel
121 A4 1_I 6 allel
122 A4 2_P 6 allel
123 A4 3_D 7 allel
124 A4 4_T 0 allel
125 A4 5_N 6 allel
126 A4 6_G 6 allel
127 A4 7_C 5 allel
128 A4 8_T 5 allel
129 A4 9_C 5 allel
130 A4 10_G 5 allel
131 A4 11_I 5 allel
132 A4 12_Q 4 allel
133 A4 13_Q 6 allel
134 A4 14_A 7 allel
135 A4 15_L 5 allel
136 A4 16_I 6 allel
137 A4 17_W 4 allel
138 A4 18_W 5 allel
139 A4 19_G 5 allel
140 A4 20_G 7 allel
141 A4 21_H 6 allel
142 A4 22_E 6 allel
143 A4 23_H 5 allel
144 A4 24_M 5 allel
145 A4 25_I 5 allel
146 A4 26_K 4 allel
147 A4 27_Q 7 allel
148 A4 28_L 5 allel
149 A4 29_L 6 allel
150 A4 30_C 6 allel
151 A4 31_I 5 allel
152 A4 32_V 7 allel
153 A4 33_H 6 allel
154 A4 34_I 5 allel
155 A4 35_C 5 allel
156 A4 36_G 5 allel
157 A4 37_E 5 allel
158 A4 38_C 5 allel
159 A4 39_N 6 allel
160 A4 40_W 6 allel
161 B1 1_I 6 allel
162 B1 2_P 1 allel
163 B1 3_D 0 allel
164 B1 4_T 6 allel
165 B1 5_N 6 allel
166 B1 6_G 4 allel
167 B1 7_C 7 allel
168 B1 8_T 6 allel
169 B1 9_C 5 allel
170 B1 10_G 7 allel
171 B1 11_I 6 allel
172 B1 12_Q 7 allel
173 B1 13_Q 5 allel
174 B1 14_A 5 allel
175 B1 15_L 5 allel
176 B1 16_I 5 allel
177 B1 17_W 7 allel
178 B1 18_W 7 allel
179 B1 19_G 6 allel
180 B1 20_G 5 allel
181 B1 21_H 6 allel
182 B1 22_E 6 allel
183 B1 23_H 5 allel
184 B1 24_M 7 allel
185 B1 25_I 6 allel
186 B1 26_K 7 allel
187 B1 27_Q 0 allel
188 B1 28_L 5 allel
189 B1 29_L 5 allel
190 B1 30_C 6 allel
191 B1 31_I 6 allel
192 B1 32_V 5 allel
193 B1 33_H 5 allel
194 B1 34_I 6 allel
195 B1 35_C 6 allel
196 B1 36_G 6 allel
197 B1 37_E 7 allel
198 B1 38_C 7 allel
199 B1 39_N 5 allel
200 B1 40_W 5 allel
201 B2 1_I 6 allel
202 B2 2_P 1 allel
203 B2 3_D 0 allel
204 B2 4_T 6 allel
205 B2 5_N 6 allel
206 B2 6_G 4 allel
207 B2 7_C 7 allel
208 B2 8_T 6 allel
209 B2 9_C 5 allel
210 B2 10_G 7 allel
211 B2 11_I 6 allel
212 B2 12_Q 7 allel
213 B2 13_Q 5 allel
214 B2 14_A 5 allel
215 B2 15_L 5 allel
216 B2 16_I 5 allel
217 B2 17_W 7 allel
218 B2 18_W 7 allel
219 B2 19_G 6 allel
220 B2 20_G 5 allel
221 B2 21_H 6 allel
222 B2 22_E 6 allel
223 B2 23_H 5 allel
224 B2 24_M 7 allel
225 B2 25_I 6 allel
226 B2 26_K 7 allel
227 B2 27_Q 0 allel
228 B2 28_L 5 allel
229 B2 29_L 5 allel
230 B2 30_C 6 allel
231 B2 31_I 6 allel
232 B2 32_V 5 allel
233 B2 33_H 5 allel
234 B2 34_I 6 allel
235 B2 35_C 6 allel
236 B2 36_G 6 allel
237 B2 37_E 7 allel
238 B2 38_C 7 allel
239 B2 39_N 5 allel
240 B2 40_W 5 allel
241 B3 1_I 5 allel
242 B3 2_P 4 allel
243 B3 3_D 5 allel
244 B3 4_T 0 allel
245 B3 5_N 4 allel
246 B3 6_G 4 allel
247 B3 7_C 4 allel
248 B3 8_T 3 allel
249 B3 9_C 5 allel
250 B3 10_G 3 allel
251 B3 11_I 4 allel
252 B3 12_Q 2 allel
253 B3 13_Q 5 allel
254 B3 14_A 5 allel
255 B3 15_L 3 allel
256 B3 16_I 5 allel
257 B3 17_W 3 allel
258 B3 18_W 5 allel
259 B3 19_G 3 allel
260 B3 20_G 5 allel
261 B3 21_H 5 allel
262 B3 22_E 4 allel
263 B3 23_H 4 allel
264 B3 24_M 4 allel
265 B3 25_I 4 allel
266 B3 26_K 2 allel
267 B3 27_Q 5 allel
268 B3 28_L 3 allel
269 B3 29_L 4 allel
270 B3 30_C 4 allel
271 B3 31_I 3 allel
272 B3 32_V 5 allel
273 B3 33_H 4 allel
274 B3 34_I 3 allel
275 B3 35_C 4 allel
276 B3 36_G 3 allel
277 B3 37_E 3 allel
278 B3 38_C 3 allel
279 B3 39_N 4 allel
280 B3 40_W 4 allel
281 B4 1_I 6 allel
282 B4 2_P 6 allel
283 B4 3_D 7 allel
284 B4 4_T 0 allel
285 B4 5_N 6 allel
286 B4 6_G 6 allel
287 B4 7_C 5 allel
288 B4 8_T 5 allel
289 B4 9_C 5 allel
290 B4 10_G 5 allel
291 B4 11_I 5 allel
292 B4 12_Q 4 allel
293 B4 13_Q 6 allel
294 B4 14_A 7 allel
295 B4 15_L 5 allel
296 B4 16_I 6 allel
297 B4 17_W 4 allel
298 B4 18_W 5 allel
299 B4 19_G 5 allel
300 B4 20_G 7 allel
301 B4 21_H 6 allel
302 B4 22_E 6 allel
303 B4 23_H 5 allel
304 B4 24_M 5 allel
305 B4 25_I 5 allel
306 B4 26_K 4 allel
307 B4 27_Q 7 allel
308 B4 28_L 5 allel
309 B4 29_L 6 allel
310 B4 30_C 6 allel
311 B4 31_I 5 allel
312 B4 32_V 7 allel
313 B4 33_H 6 allel
314 B4 34_I 5 allel
315 B4 35_C 5 allel
316 B4 36_G 5 allel
317 B4 37_E 5 allel
318 B4 38_C 5 allel
319 B4 39_N 6 allel
320 B4 40_W 6 allel
321 A1 1_I 6 not allel
322 A1 2_P 6 not allel
323 A1 3_D 7 not allel
324 A1 4_T 0 not allel
325 A1 5_N 6 not allel
326 A1 6_G 6 not allel
327 A1 7_C 5 not allel
328 A1 8_T 5 not allel
329 A1 9_C 5 not allel
330 A1 10_G 5 not allel
331 A1 11_I 5 not allel
332 A1 12_Q 4 not allel
333 A1 13_Q 6 not allel
334 A1 14_A 7 not allel
335 A1 15_L 5 not allel
336 A1 16_I 6 not allel
337 A1 17_W 4 not allel
338 A1 18_W 5 not allel
339 A1 19_G 5 not allel
340 A1 20_G 7 not allel
341 A1 21_H 6 not allel
342 A1 22_E 6 not allel
343 A1 23_H 5 not allel
344 A1 24_M 5 not allel
345 A1 25_I 5 not allel
346 A1 26_K 4 not allel
347 A1 27_Q 7 not allel
348 A1 28_L 5 not allel
349 A1 29_L 6 not allel
350 A1 30_C 6 not allel
351 A1 31_I 5 not allel
352 A1 32_V 7 not allel
353 A1 33_H 6 not allel
354 A1 34_I 5 not allel
355 A1 35_C 5 not allel
356 A1 36_G 5 not allel
357 A1 37_E 5 not allel
358 A1 38_C 5 not allel
359 A1 39_N 6 not allel
360 A1 40_W 6 not allel
361 A2 1_I 10 not allel
362 A2 2_P 6 not allel
363 A2 3_D 7 not allel
364 A2 4_T 3 not allel
365 A2 5_N 9 not allel
366 A2 6_G 8 not allel
367 A2 7_C 9 not allel
368 A2 8_T 8 not allel
369 A2 9_C 8 not allel
370 A2 10_G 9 not allel
371 A2 11_I 9 not allel
372 A2 12_Q 8 not allel
373 A2 13_Q 9 not allel
374 A2 14_A 9 not allel
375 A2 15_L 8 not allel
376 A2 16_I 8 not allel
377 A2 17_W 8 not allel
378 A2 18_W 9 not allel
379 A2 19_G 8 not allel
380 A2 20_G 10 not allel
381 A2 21_H 9 not allel
382 A2 22_E 9 not allel
383 A2 23_H 9 not allel
384 A2 24_M 9 not allel
385 A2 25_I 8 not allel
386 A2 26_K 8 not allel
387 A2 27_Q 7 not allel
388 A2 28_L 9 not allel
389 A2 29_L 8 not allel
390 A2 30_C 9 not allel
391 A2 31_I 9 not allel
392 A2 32_V 9 not allel
393 A2 33_H 8 not allel
394 A2 34_I 8 not allel
395 A2 35_C 8 not allel
396 A2 36_G 9 not allel
397 A2 37_E 9 not allel
398 A2 38_C 9 not allel
399 A2 39_N 8 not allel
400 A2 40_W 9 not allel
401 A3 1_I 6 not allel
402 A3 2_P 1 not allel
403 A3 3_D 0 not allel
404 A3 4_T 6 not allel
405 A3 5_N 6 not allel
406 A3 6_G 4 not allel
407 A3 7_C 7 not allel
408 A3 8_T 6 not allel
409 A3 9_C 5 not allel
410 A3 10_G 7 not allel
411 A3 11_I 6 not allel
412 A3 12_Q 7 not allel
413 A3 13_Q 5 not allel
414 A3 14_A 5 not allel
415 A3 15_L 5 not allel
416 A3 16_I 5 not allel
417 A3 17_W 7 not allel
418 A3 18_W 7 not allel
419 A3 19_G 6 not allel
420 A3 20_G 5 not allel
421 A3 21_H 6 not allel
422 A3 22_E 6 not allel
423 A3 23_H 5 not allel
424 A3 24_M 7 not allel
425 A3 25_I 6 not allel
426 A3 26_K 7 not allel
427 A3 27_Q 0 not allel
428 A3 28_L 5 not allel
429 A3 29_L 5 not allel
430 A3 30_C 6 not allel
431 A3 31_I 6 not allel
432 A3 32_V 5 not allel
433 A3 33_H 5 not allel
434 A3 34_I 6 not allel
435 A3 35_C 6 not allel
436 A3 36_G 6 not allel
437 A3 37_E 7 not allel
438 A3 38_C 7 not allel
439 A3 39_N 5 not allel
440 A3 40_W 5 not allel
441 A4 1_I 6 not allel
442 A4 2_P 1 not allel
443 A4 3_D 0 not allel
444 A4 4_T 6 not allel
445 A4 5_N 6 not allel
446 A4 6_G 4 not allel
447 A4 7_C 7 not allel
448 A4 8_T 6 not allel
449 A4 9_C 5 not allel
450 A4 10_G 7 not allel
451 A4 11_I 6 not allel
452 A4 12_Q 7 not allel
453 A4 13_Q 5 not allel
454 A4 14_A 5 not allel
455 A4 15_L 5 not allel
456 A4 16_I 5 not allel
457 A4 17_W 7 not allel
458 A4 18_W 7 not allel
459 A4 19_G 6 not allel
460 A4 20_G 5 not allel
461 A4 21_H 6 not allel
462 A4 22_E 6 not allel
463 A4 23_H 5 not allel
464 A4 24_M 7 not allel
465 A4 25_I 6 not allel
466 A4 26_K 7 not allel
467 A4 27_Q 0 not allel
468 A4 28_L 5 not allel
469 A4 29_L 5 not allel
470 A4 30_C 6 not allel
471 A4 31_I 6 not allel
472 A4 32_V 5 not allel
473 A4 33_H 5 not allel
474 A4 34_I 6 not allel
475 A4 35_C 6 not allel
476 A4 36_G 6 not allel
477 A4 37_E 7 not allel
478 A4 38_C 7 not allel
479 A4 39_N 5 not allel
480 A4 40_W 5 not allel
481 B1 1_I 6 not allel
482 B1 2_P 6 not allel
483 B1 3_D 7 not allel
484 B1 4_T 0 not allel
485 B1 5_N 6 not allel
486 B1 6_G 6 not allel
487 B1 7_C 5 not allel
488 B1 8_T 5 not allel
489 B1 9_C 5 not allel
490 B1 10_G 5 not allel
491 B1 11_I 5 not allel
492 B1 12_Q 4 not allel
493 B1 13_Q 6 not allel
494 B1 14_A 7 not allel
495 B1 15_L 5 not allel
496 B1 16_I 6 not allel
497 B1 17_W 4 not allel
498 B1 18_W 5 not allel
499 B1 19_G 5 not allel
500 B1 20_G 7 not allel
501 B1 21_H 6 not allel
502 B1 22_E 6 not allel
503 B1 23_H 5 not allel
504 B1 24_M 5 not allel
505 B1 25_I 5 not allel
506 B1 26_K 4 not allel
507 B1 27_Q 7 not allel
508 B1 28_L 5 not allel
509 B1 29_L 6 not allel
510 B1 30_C 6 not allel
511 B1 31_I 5 not allel
512 B1 32_V 7 not allel
513 B1 33_H 6 not allel
514 B1 34_I 5 not allel
515 B1 35_C 5 not allel
516 B1 36_G 5 not allel
517 B1 37_E 5 not allel
518 B1 38_C 5 not allel
519 B1 39_N 6 not allel
520 B1 40_W 6 not allel
521 B2 1_I 6 not allel
522 B2 2_P 6 not allel
523 B2 3_D 7 not allel
524 B2 4_T 0 not allel
525 B2 5_N 6 not allel
526 B2 6_G 6 not allel
527 B2 7_C 5 not allel
528 B2 8_T 5 not allel
529 B2 9_C 5 not allel
530 B2 10_G 5 not allel
531 B2 11_I 5 not allel
532 B2 12_Q 4 not allel
533 B2 13_Q 6 not allel
534 B2 14_A 7 not allel
535 B2 15_L 5 not allel
536 B2 16_I 6 not allel
537 B2 17_W 4 not allel
538 B2 18_W 5 not allel
539 B2 19_G 5 not allel
540 B2 20_G 7 not allel
541 B2 21_H 6 not allel
542 B2 22_E 6 not allel
543 B2 23_H 5 not allel
544 B2 24_M 5 not allel
545 B2 25_I 5 not allel
546 B2 26_K 4 not allel
547 B2 27_Q 7 not allel
548 B2 28_L 5 not allel
549 B2 29_L 6 not allel
550 B2 30_C 6 not allel
551 B2 31_I 5 not allel
552 B2 32_V 7 not allel
553 B2 33_H 6 not allel
554 B2 34_I 5 not allel
555 B2 35_C 5 not allel
556 B2 36_G 5 not allel
557 B2 37_E 5 not allel
558 B2 38_C 5 not allel
559 B2 39_N 6 not allel
560 B2 40_W 6 not allel
561 B3 1_I 7 not allel
562 B3 2_P 3 not allel
563 B3 3_D 2 not allel
564 B3 4_T 6 not allel
565 B3 5_N 8 not allel
566 B3 6_G 6 not allel
567 B3 7_C 8 not allel
568 B3 8_T 8 not allel
569 B3 9_C 5 not allel
570 B3 10_G 9 not allel
571 B3 11_I 7 not allel
572 B3 12_Q 9 not allel
573 B3 13_Q 6 not allel
574 B3 14_A 7 not allel
575 B3 15_L 7 not allel
576 B3 16_I 6 not allel
577 B3 17_W 8 not allel
578 B3 18_W 7 not allel
579 B3 19_G 8 not allel
580 B3 20_G 7 not allel
581 B3 21_H 7 not allel
582 B3 22_E 8 not allel
583 B3 23_H 6 not allel
584 B3 24_M 8 not allel
585 B3 25_I 7 not allel
586 B3 26_K 9 not allel
587 B3 27_Q 2 not allel
588 B3 28_L 7 not allel
589 B3 29_L 7 not allel
590 B3 30_C 8 not allel
591 B3 31_I 8 not allel
592 B3 32_V 7 not allel
593 B3 33_H 7 not allel
594 B3 34_I 8 not allel
595 B3 35_C 7 not allel
596 B3 36_G 8 not allel
597 B3 37_E 9 not allel
598 B3 38_C 9 not allel
599 B3 39_N 7 not allel
600 B3 40_W 7 not allel
601 B4 1_I 6 not allel
602 B4 2_P 1 not allel
603 B4 3_D 0 not allel
604 B4 4_T 6 not allel
605 B4 5_N 6 not allel
606 B4 6_G 4 not allel
607 B4 7_C 7 not allel
608 B4 8_T 6 not allel
609 B4 9_C 5 not allel
610 B4 10_G 7 not allel
611 B4 11_I 6 not allel
612 B4 12_Q 7 not allel
613 B4 13_Q 5 not allel
614 B4 14_A 5 not allel
615 B4 15_L 5 not allel
616 B4 16_I 5 not allel
617 B4 17_W 7 not allel
618 B4 18_W 7 not allel
619 B4 19_G 6 not allel
620 B4 20_G 5 not allel
621 B4 21_H 6 not allel
622 B4 22_E 6 not allel
623 B4 23_H 5 not allel
624 B4 24_M 7 not allel
625 B4 25_I 6 not allel
626 B4 26_K 7 not allel
627 B4 27_Q 0 not allel
628 B4 28_L 5 not allel
629 B4 29_L 5 not allel
630 B4 30_C 6 not allel
631 B4 31_I 6 not allel
632 B4 32_V 5 not allel
633 B4 33_H 5 not allel
634 B4 34_I 6 not allel
635 B4 35_C 6 not allel
636 B4 36_G 6 not allel
637 B4 37_E 7 not allel
638 B4 38_C 7 not allel
639 B4 39_N 5 not allel
640 B4 40_W 5 not allel
Saving 6.67 x 6.67 in image
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.