getfreqs: Get frequencies for amino acids/nucleotides in alignment...

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

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getfreqs(path_to_file_sequence_alignment = NULL, save_csv, save_png, 
 epitope_position_start, epitope_position_end,
 path_to_file_consensus, patnum_threshold = 1, A11, A12, A21, A22,
 B11, B12, B21, B22, one_feature=FALSE)

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

assocpoint

Examples

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#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:BiocGenericsThe following objects are masked frompackage:parallel:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage: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:S4VectorsThe following objects are masked frompackage:tcltk2:

    values, values<-

The following object is masked frompackage:base:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package:BiostringsThe following object is masked frompackage: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.