-
Notifications
You must be signed in to change notification settings - Fork 0
/
consen_14.Rproj
512 lines (512 loc) · 24.7 KB
/
consen_14.Rproj
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
arya_loci_lg2<-arya_loci[13:22]
arya_name_lg2<-arya_name[13:32]
arya_name_lg1<-arya_name[2:10]
arya_loci_lg3<-arya_loci[35:56]
arya_name_lg3<-arya_name[35:56]
arya_name_lg4<-arya_name[59:71]
arya_name_lg1<-arya_name[2:10]
arya_name_lg2<-arya_name[13:32]
arya_name_lg3<-arya_name[35:56]
arya_name_lg4<-arya_name[59:71]
arya_name_lg5<-arya_name[74:95]
arya_name_lg6<-arya_name[97:123]
arya_name_lg7<-arya_name[126:147]
arya_name_lg8<-arya_name[150:156]
arya_loci_lg1<-arya_loci[2:!0]
arya_loci_lg2<-arya_loci[13:32]
arya_loci_lg1<-arya_loci[2:10]
arya_loci_lg3<-arya_loci[35:56]
arya_loci_lg4<-arya_loci[59:71]
arya_loci_lg5<-arya_loci[74:95]
arya_loci_lg6<-arya_loci[97:123]
arya_loci_lg7<-arya_loci[126:147]
arya_loci_lg8<-arya_loci[150:156]
kotta_name_lg1<-kotta_name[2:10]
kotta_name_lg2<-kotta_name[13:28]
kotta_name_lg3<-kotta_name[30:39]
kotta_name_lg4<-kotta_name[42:52]
kotta_name_lg5a<-kotta_name[55:61]
kotta_name_lg5b<-kotta_name[64:67]
kotta_name_lg6<-kotta_name[70:83]
kotta_name_lg7<-kotta_name[86:93]
kotta_name_lg8a<-kotta_name[96:99]
kotta_name_lg8b<-kotta_name[102:103]
kotta_loci_lg1<-kotta_loci[2:10]
kotta_loci_lg3<-kotta_loci[30:39]
kotta_loci_lg4<-kotta_loci[42:52]
kotta_loci_lg5a<-kotta_loci[55:61]
kotta_loci_lg5b<-kotta_loci[64:67]
kotta_loci_lg6<-kotta_loci[70:83]
kotta_loci_lg7<-kotta_loci[86:93]
kotta_loci_lg8a<-kotta_loci[96:99]
kotta_loci_lg8b<-kotta_loci[102:103]
cobos_name_lg1<-cobos_name[2:10]
cobos_name_lg2<-cobos_name[13:22]
cobos_name_lg3<-cobos_name[25:37]
cobos_name_lg4<-cobos_name[40:59]
cobos_name_lg5<-cobos_name[62:71]
cobos_name_lg7_8<-cobos_name[74:87]
cobos_loci_lg2<-cobos_loci[13:22]
cobos_loci_lg1<-cobos_loci[2:10]
cobos_loci_lg3<-cobos_loci[25:37]
cobos_loci_lg4<-cobos_loci[40:59]
cobos_loci_lg5<-cobos_loci[62:71]
cobos_loci_lg7_8<-cobos_loci[74:87]
sabba_Ab_loci_lg8<-sabba_ab_loci[67:69]
sabba_Ab_loci_lg7<-sabba_ab_loci[63:64]
sabba_Ab_loci_lg6<-sabba_ab_loci[47:60]
sabba_Ab_loci_lg5<-sabba_ab_loci[39:44]
sabba_Ab_loci_lg4<-sabba_ab_loci[26:36]
sabba_Ab_loci_lg3<-sabba_ab_loci[18:23]
sabba_Ab_loci_lg2<-sabba_ab_loci[7:15]
sabba_Ab_loci_lg1<-sabba_ab_loci[2:4]
sabba_ab_name_lg7<-sabba_Ab_name[63:64]
sabba_Ab_name_lg6<-sabba_ab_name[47:60]
asbba_Ab_name_lg5<-sabba_ab_name[39:44]
sabba_ab_name_lg7<-sabba_ab_name[63:64]
asbba_Ab_name_lg5<-sabba_ab_name[39:44]
sabba_Ab_name_lg6<-sabba_ab_name[47:60]
asbba_Ab_name_lg5<-sabba_ab_name[39:44]
sabba_ab_name_lg2<-sabba_ab_name[7:15]
sabba_ab_name_lg3<-sabba_ab_name[18:23]
sabba_Ab_name_lg4<-sabba_ab_name[26:36]
sabba_Ab_name_lg8<-sabba_ab_name[67:69]
sabba_Ab_loci_lg8<-sabba_ab_loci[67:69]
sabba_Ab_loci_lg7<-sabba_ab_loci[63:64]
sabba_Ab_loci_lg6<-sabba_ab_loci[47:60]
sabba_Ab_loci_lg5<-sabba_ab_loci[39:44]
sabba_Ab_loci_lg4<-sabba_ab_loci[26:36]
sabba_Ab_loci_lg3<-sabba_ab_loci[18:23]
sabba_Ab_loci_lg2<-sabba_ab_loci[7:15]
sabba_Ab_loci_lg1<-sabba_ab_loci[2:4]
View(varshney_fw_lg4)
save.image("C:/Users/ishit/OneDrive/Documents/Chickpea/consensus_dev.RData")
irulena_loci_lg1<-irulena_loci[2:13]
irulena_name_lg1<-irulena_name[2:13]
irulena_lg2<-data.frame(marker=irulena_name_lg1,position=irulena_loci_lg1)
taran_loci_lg1<-taran_loci[2:11]
taran_loci_lg3<-taran_loci[32:56]
taran_loci_lg2<-taran_loci[14:29]
taran_loci_lg4<-taran_loci[59:80]
taran_loci_lg5<-taran_loci[83:105]
taran_loci_lg6<-taran_loci[108:125]
taran_loci_lg7<-taran_loci[128:148]
taran_loci_lg8<-taran_loci[151:160]
taran_name_lg1<-taran_name[2:11]
taran_name_lg2<-taran_name[14:29]
taran_name_lg3<-taran_name[32:56]
taran_name_lg4<-taran_name[59:80]
taran_name_lg5<-tran_name[83:!05]
taran_name_lg5<-tran_name[83:105]
taran_name_lg5<-taran_name[83:105]
taran_name_lg6<-taran_name[108:125]
taran_name_lg7<-taran_name[128:148]
taran_name_lg8<-taran_name[151:160]
taran_lg8<-data.frame(marker=taran_name_lg8,position=taran_loci_lg8)
taran_lg7<-data.frame(marker=taran_name_lg7,position=taran_loci_lg7)
taran_lg6<-data.frame(marker=taran_name_lg6,position=taran_loci_lg6)
taran_lg4<-data.frame(marker=taran_name_lg4,position=taran_loci_lg4)
taran_lg5<-data.frame(marker=taran_name_lg5,position=taran_loci_lg5)
taran_lg3<-data.frame(marker=taran_name_lg3,position=taran_loci_lg3)
taran_lg2<-data.frame(marker=taran_name_lg2,position=taran_loci_lg2)
taran_lg1<-data.frame(marker=taran_name_lg1,position=taran_loci_lg2)
taran_lg1<-data.frame(marker=taran_name_lg1,position=taran_loci_lg1)
anupama_loci_lg8<-anupama_loci[70:73]
anupama_loci_lg7<-anupama_loci[63:67]
anupama_loci_lg6<-anupama_loci[51:60]
anupama_loci_lg5<-anupama_loci[42:48]
anupama_loci_lg4<-anupama_loci[28:39]
anupama_loci_lg3b<-anupama_loci[21:24]
anupama_loci_lg3a<-anupama_loci[17:18]
anupama_loci_lg2<-anupama_loci[11:14]
anupama_loci_lg1<-anupama_loci[3:8]
anupama_name_lg8<-anupama_name[70:73]
anupama_name_lg7<-anupama_name[63:67]
anupama_name_lg6<-anupama_name[51:60]
anupama_name_lg5<-anupama_name[42:48]
anupama_name_lg4<-anupama_name[28:39]
anupama_name_lg3b<-anupama_name[21:24]
anupama_name_lg3a<-anupama_name[17:18]
anupama_name_lg2<-anupama_name[11:14]
anupama_name_lg1<-anupama_name[3:8]
anupama_lg8<-data.frame(marker=anupama_name_lg8,poisiton=anupama_loci_lg8)
anupama_lg7<-data.frame(marker=anupama_name_lg7,position=anupama_loci_lg7)
anupama_lg6<-data.frame(marker=anupama_name_lg6,position=anupama_loci_lg6)
anupama_lg5<-data.frame(marker=anupama_name_lg5,position=anupama_loci_lg5)
anupmam_lg4<-data.frame(marker=anupama_name_lg4,position=anupama_lg4)
anupama_lg3b<-data.frame(marker=anupama_name_lg3b,position=anupama_loci_lg3b)
anupama_lg3a<-data.frame(marker=anupama_name_lg3a,position=anupama_loci_lg3a)
anupama_lg2<-data.frame(marker=anupama_name_lg2,position=anupama_loci_lg2)
anupama_lg1<-data.frame(marker=anupama_name_lg1,position=anupama_loci_lg1)
tosh_loci_lg8<-tosh_loci[194:202]
tosh_loci_lg7<-tosh_loci[172:191]
tosh_loci_lg6<-tosh_loci[127:169]
tosh_loci_lg5<-tosh_loci[94:124]
tosh_loci_lg4<-tosh_loci[64:91]
tosh_loci_lg3<-tosh_loci[45:61]
tosh_loci_lg2<-tosh_loci[28:42]
tosh_loci_lg1<-tosh_loci[2:25]
tosh_name_lg8<-tosh_name[194:202]
tosh_name_lg7<-tosh_name[172:191]
tosh_name_lg6<-tosh_name[127:169]
tosh_name_lg5<-tosh_name[94:124]
tosh_name_lg4<-tosh_name[64:91]
tosh_name_lg3<-tosh_name[45:61]
tosh_name_lg2<-tosh_name[28:42]
tosh_name_lg1<-tosh_name[2:25]
tosh_lg8<-data.frame(marker=tosh_name_lg8,position=tosh_loci_lg8)
tosh_lg7<-data.frame(marker=tosh_name_lg7,position=tosh_loci_lg7)
tosh_lg6<-data.frame(marker=tosh_name_lg6,position=tosh_loci_lg6)
tosh_lg5<-data.frame(marker=tosh_name_lg5,position=tosh_loci_lg5)
tosh_lg4<-data.frame(marker=tosh_name_lg4,position=tosh_loci_lg4)
tosh_lg3<-data.frame(marker=tosh_name_lg3,positon=tosh_loci_lg3)
tosh_lg2<-data.frame(marker=tosh_name_lg2,position=tosh_loci_lg2)
tosh_lg1<-data.frame(marker=tosh_name_lg1,position=tosh_loci_lg1)
anuradha_loci_lg6<-anuradha_loci[18:36]
anuradha_loci_lg6<-anurahda_loci[18:36]
anuradha_loci_lg6<-anuradha_loci[18:36]
anuradha_loci_lg3<-anuradha_loci[2:15]
anuradha_name_lg6<-anuradha_name[18:36]
anuradha_name_lg3<-anuradha_name[2:15]
anuradha_lg6<-data.frame(marker=anuradha_name_lg6,position=anuradha_loci_lg6)
anuradha_lg3<-data.frame(marker=anuradha_name_lg3,position=anuradha_loci_lg3)
daba_loci_lg8<-daba_loci[326:362]
daba_loci_lg7<-daba_loci[275:323]
daba_loci_lg6<-daba_loci[231:272]
daba_loci_lg5<-daba_loci[201:228]
daba_loci_lg4<-daba_loci[134:198]
daba_loci_lg3<-daba_loci[92:131]
daba_loci_lg2<-daba_loci[43:89]
daba_loci_lg1<-daba_loci[2:40]
daba_name_lg8<-daba_name[326:362]
daba_name_lg7<-daba_name[275:323]
daba_name_lg6<-daba_name[231:272]
daba_name_lg5<-daba_name[201:228]
daba_name_lg4<-daba_name[134:198]
daba_name_lg3<-daba_name[92:131]
daba_name_lg2<-daba_name[43:89]
daba_name_lg1<-daba_name[2:40]
sabba_fw_loci_lg8<-sabba_fw_loci[72:76]
sabba_fw_loci_lg7<-sabba_fw_loci[64:69]
sabba_fw_loci_lg6<-sabba_fw_loci[52:61]
sabba_fw_loci_lg5<-sabba_fw_loci[42:49]
sabba_fw_loci_lg4<-sabba_fw_loci[29:39]
sabba_fw_loci_lg3<-sabba_fw_loci[20:26]
sabba_fw_loci_lg2<-sabba_fw_loci[7:17]
sabba_fw_loci_lg1<-sabba_fw_loci[2:4]
sabba_fw_loci_lg1<sabba_fw_loci[2:4]
sabba_fw_loci_lg1<-sabba_fw_loci[2:4]
sabba_fw_name_lg8<-sabba_fw_name[72:76]
sabba_fw_name_lg7<-sabba_fw_name[64:69]
sabba_fw_name_lg6<-sabba_fw_name[52:61]
sabba_fw_name_lg5<-sabba_fw_name[42:49]
sabba_fw_name_lg4<-sabba_fw_name[29:39]
sabba_fw_name_lg3<-sabba_fw_name[20:26]
sabba_fw_name_lg2<-sabba_fw_name[7:17]
sabba_fw_name_lg1<-sabba_fw_name[2:4]
sabba_fw_lg8<-data.frame(marker=sabba_fw_name_lg8,position=sabba_fw_loci_lg8)
sabba_fw_lg7<-data.frame(marker=sabba_fw_name_lg7,position=sabba_fw_loci_lg7)
sabba_fw_lg7<-data,frame(marker=sabba_fw_name_lg7,position=sabba_fw_loci_lg7)
sabba_fw_lg7<-data.frame(marker=sabba_fw_name_lg7,position=sabba_fw_loci_lg7)
sabba_fw_lg1<-data.frame(marker=sabba_fw_name_lg1,position=sabba_fw_loci_lg1)
sabba_fw_lg2<-data.frame(marker=sabba_fw_name_lg2,sabba_fw_loci_lg2)
sabba_fw_lg3<-data.frame(marker=sabba_fw_loci_lg3,position=sabba_fw_loci_lg3)
sabba_fw_lg4<-data.frame(marker=sabba_fw_name_lg4,position=sabba_fw_loci_lg4)
sabba_fw_lg5<-data.frame(marker=sabba_fw_name_lg5,position=sabba_fw_loci_lg5)
sabba_fw_lg6<-data.frame(marker=sabba_fw_name_lg6,position=sabba_fw_loci_lg6)
muehlbauer_loci_lg2<-muehlbauer_loci[2:10]
muehlbauer_name_lg2<-muehlbauer_name[2:10]
muehlbauer_lg2<-data.frame(marker=muehlbauer_name_lg2,position=muehlbauer_loci_lg2)
halila_name_lg2<-halila_name[2:13]
halila_loci_lg2<-halila_loci[2:13]
halila_lg2<-data.frame(marker=halila_name_lg2,position=halila_loci_lg2)
gowda_name_lg2<-gowda_name[2:23]
gowda_loci_lg2<-gowda_loci[2:23]
gowda_lg2<-data.frame(marker=gowda_name_lg2,position=gowda_loci_lg2)
palomino_loci_lg8<-palomino_loci[182:191]
palomino_loci_lg7<-palomino_loci[164:178]
palomino_loci_lg6<-palomino_loci[150:161]
palomino_loci_lg5<-palomino_loci[118:147]
palomino_loci_lg4<-palomino_loci[81:115]
palomino_loci_lg3<-palomino_loci[41:78]
palomino_loci_lg2<-palomino_loci[16:38]
palomino_loci_lg1<-palomino_loci[2:13]
palomino_name_lg8<-palomino_name[182:191]
palomino_name_lg7<-palomino_name[164:178]
palomino_name_lg6<-palomino_name[150:161]
palomino_name_lg5<-palomino_name[118:147]
palomino_name_lg4<-palomino_name[81:115]
palomino_name_lg3<-palomino_name[41:78]
palomino_name_lg2<-palomino_name[16:38]
palomino_name_lg1<-palomino_name[2:13]
palomino_lg1<-data.frame(marker=palomino_name_lg1,position=palomino_loci_lg2)
palomino_lg1<-data.frame(marker=palomino_name_lg1,position=palomino_loci_lg1)
palomino_lg2<-data.frame(marker=palomino_name_lg2,position=palomino_loci_lg2)
palomino_lg3<-data.frame(marker=palomino_name_lg3,position=palomino_loci_lg3)
palomino_lg4<-data.frame(marker=palomino_name_lg4,position=palomino_loci_lg4)
palomino_lg5<-data.frame(marker=palomino_name_lg5,position=palomino_loci_lg5)
palomino_lg6<-data.frame(marker=palomino_name_lg6,position=palomino_loci_lg6)
palomino_lg7<-data.frame(marker=palomino_name_lg7,position=palomino_loci_lg7)
palomino_lg8<-data.frame(marker=palomino_name_lg8,position=palomino_loci_lg8)
santra_loci_lg8<-santra_loci[103:117]
santra_loci_lg7<-santra_loci[83:100]
santra_loci_lg6<-santra_loci[76:79]
santra_loci_lg5<-santra_loci[59:73]
santra_loci_lg4<-santra_loci[43:56]
santra_loci_lg3<-santra_loci[18:40]
santra_loci_lg2<-santra_loci[12:15]
santra_loci_lg1<-santra_loci[2:9]
santra_name_lg8<-santra_name[103:117]
santra_name_lg7<-santra_name[83:100]
santra_name_lg6<-santra_name[76:79]
santra_name_lg5<-santra_name[59:73]
santra_name_lg4<-santra_name[43:56]
santra_name_lg3<-santra_name[18:40]
santra_name_lg2<-santra_name[12:15]
santra_name_lg1<-santra_name[2:9]
santra_lg1<-data.frame(marker=santra_name_lg1,position=santra_loci_lg1)
santra_lg2<-data.frame(marker=santra_name_lg2,position=santra_loci_lg2)
santra_lg3<-data.frame(marker=santra_name_lg3,position=santra_loci_lg3)
santra_lg4<-data.frame(marker=santra_name_lg4,position=santra_loci_lg4)
santra_lg5<-data.frame(marker=santra_name_lg5,position=santra_loci_lg5)
santra_lg6<-data.frame(marker=santra_name_lg6,position=santra_loci_lg6)
santra_lg7<-data.frame(marker=santra_name_lg7,position=santra_loci_lg7)
santra_lg8<-data.frame(marker=santra_name_lg8,position=santra_loci_lg8)
patil_loci_lg5<-patil_loci[30:32]
patil_loci_lg4<-patil_loci[24:27]
patil_loci_lg3<-patil_loci[16:21]
patil_loci_lg2<-patil_loci[6:13]
patil_loci_lg1<-patil_loci[2:3]
patil_name_lg5<-patil_name[30:32]
patil_name_lg4<-patil_name[24:27]
patil_name_lg3<-patil_name[16:21]
patil_name_lg2<-patil_name[6:13]
patil_name_lg1<-patil_name[2:3]
patil_lg1<-data.frame(marker=patil_name_lg1,position=patil_loci_lg1)
patil_lg2<-data.frame(marker=patil_name_lg2,position=patil_loci_lg2)
patil_lg3<-data.frame(marker=patil_name_lg3,position=patil_loci_lg3)
patil_lg4<-data.frame(marker=patil_name_lg4,position=patil_loci_lg4)
patil_lg5<-data.frame(marker=patil_name_lg5,position=patil_loci_lg5)
patil_lg6<-data.frame(marker=patil_name_lg6,position=patil_loci_lg6)
winter_name_lg1<-winter_name[2:40]
winter_name_lg2<-winter_name[43:78]
winter_name_lg3<-winter_name[81:123]
winter_name_lg4<-winter_name[126:162]
winter_name_lg5<-winter_name[165:206]
winter_name_lg6<-winter_name[209:242]
winter_name_lg7<-winter_name[245:271]
winter_name_lg8<-winter_name[274:1=297]
winter_name_lg8<-winter_name[274:287]
winter_loci_lg1<-winter_name[2:40]
winter_loci_lg2<-winter_loci[43:78]
winter_loci_lg3<-winter_loci[81:123]
winter_loci_lg4<-winter_loci[126:162]
winter_loci_lg5<-winter_loci[165:206]
winter_loci_lg6<-winter_loci[209:242]
winter_loci_lg7<-winter_loci[245:271]
winter_loci_lg8<-winter_loci[274:287]
winter_lg1<-data.frame(marker=winter_name_lg1,position=winter_loci_lg1)
winter_lg2<-data.frame(marker=winter_name_lg2,position=winter_loci_lg2)
winter_lg3<-data.frame(marker=winter_name_lg3,position=winter_loci_lg3)
winter_lg4<-data.frame(marker=winter_name_lg4,poistion=winter_loci_lg4)
winter_lg5<-data.frame(marker=winter_name_lg5,position=winter_loci_lg5
winter_lg6<-data.frame(marker=winter_name_lg6,position=winter_loci_lg6)
winter_lg7<-data.frame(marker=winter_name_lg7,position=winter_loci_lg7)
winter_lg8<-data.frame(marker=winter_name_lg8,position=winter_loci_lg8)
winter_lg6<-data.frame(marker=winter_name_lg6,position=winter_loci_lg6)
winter_lg5<-data.frame(marker=winter_name_lg5,position=winter_loci_lg5)
galvez_loci_lg8<-galvez_loci[79:80]
galvez_loci_lg7<-galvez_loci[71:76]
galvez_loci_lg6<-galvez_loci[60:68]
galvez_loci_lg5<-galvez_loci[52:57]
galvez_loci_lg4<-galvez_loci[45:49]
galvez_loci_lg3<-galvez_loci[33:42]
galvez_loci_lg2<-galvez_loci[22:30]
galvez_loci_lg1<-galvez_loci[2:19]
galvez_name_lg8<-galvez_name[79:80]
galvez_name_lg7<-galvez_name[71:76]
galvez_name_lg6<-galvez_name[60:68]
galvez_name_lg6<-galvez_name[52:57]
galvez_name_lg5<-galvez_name[52:57]
galvez_name_lg6<-galvez_name[60:68]
galvez_name_lg4<-galvez_name[45:49]
galvez_name_lg3<-galvez_name[33:42]
galvez_name_lg2<-galvez_name[22:30]
galvez_name_lg1<-galvez_name[2:19]
galvez_loci_lg8<-galvez_loci[79:80]
galvez_loci_lg7<-galvez_loci[71:76]
galvez_loci_lg6<-galvez_loci[60:68]
galvez_loci_lg5<-galvez_loci[52:57]
galvez_loci_lg4<-galvez_loci[45:49]
galvez_loci_lg3<-galvez_loci[33:42]
galvez_loci_lg2<-galvez_loci[22:30]
galvez_loci_lg1<-galvez_loci[2:19]
galvez_lg1<-data.frame(marker=galvez_name_lg1,position=galvez_loci_lg1)
galvez_lg2<-data.frame(marker=galvez_name_lg2,position=galvez_loci_lg2)
galvez_lg3<-data.frame(marker=galvez_name_lg3,position=galvez_loci_lg3)
galvez_lg4<-data.frame(marker=galvez_name_lg4,position=galvez_loci_lg4)
galvez_lg5<-data.frame(marker=galvez_name_lg5,position=galvez_loci_lg5)
galvez_lg6<-data.frame(marker=galvez_name_lg6,position=galvez_loci_lg6)
galvez_lg7<-data.frame(marker=galvez_name_lg7,position=galvez_loci_lg7)
galvez_lg8<-data.frame(marker=galvez_name_lg8,position=galvez_loci_lg8)
tekolgu_loci_lg8<-tekolgu_loci[17:22]
tekolgu_name_lg8<-tekolgu_name[17:22]
tekolgu_loci_lg4<-tekolgu_loci[2:14]
tekolgu_name_lg4<-tekolgu_name[2:14]
tekolgy_lg4<-data.frame(marker=tekolgu_name_lg4,position=tekolgu_loci_lg4)
tekolgu_lg8<-data.frame(marker=tekolgu_name_lg8,position=tekolgu_loci_lg8)
stephens_name_lg4.3<-stephens_name[117:123]
stephens_name_lg4.2<-stephens_name[66:114]
stephens_name_lg4.1<-stephens_name[2:63]
stephens_loci_lg4.2<-stephens_loci[66:114]
stephens_loci_lg4.3<-stephens_loci[117:123]
stephens_loci_lg4.1<-stephens_loci[2:63]
stephens_lg4.1<-data.frame(marker=stephens_name_lg4.1,position=stephens_loci_lg4.1)
stephens_lg4.2<-data.frame
stephens_lg4.2<-data.frame(marker=stephens_name_lg4.2,position=stephens_loci_lg4.2)
stephens_lg4.3<-data.frame(marker=stephens_name_lg4.3,position=stephens_loci_lg4.3
stephens_lg4.3<-data.frame(marker=stephens_name_lg4.3,position=stephens_loci_lg4.3
stephens_lg4.3<-data.frame(marker=stephens_name_lg4.3,position=stephens_loci_lg4.3)
list_lg1<-list(arya_lg1,kotta_lg1,cobos_lg1,sabba_fw_lg1,taran_lg1,anupama_lg1,tosh_lg1,daba_lg1,palomino_lg1,santra_lg1,patil_lg1,winter_lg1,galvez_lg1)
sabba_ab_lg2<-data.frame(marker=sabba_ab_name_lg2,position=sabba_Ab_loci_lg2)
sabba_ab_lg3<-data.frame(marker=sabba_ab_name_lg3,position=sabba_Ab_loci_lg3)
sabba_ab_lg4<-data.frame(marker=sabba_ab_name_lg4,position=sabba_Ab_loci_lg4)
sabba_ab_lg4<-data.frame(marker=sabba_Ab_name_lg4,position=sabba_Ab_loci_lg4)
sabba_ab_lg5<-data.frame(marker=sabba_Ab_name_lg5,position=sabba_Ab_loci_lg5)
sabba_ab_lg6<-data.frame(marker=sabba_Ab_name_lg6,position=sabba_Ab_loci_lg6)
sabba_ab_lg7<-data.frame(marker=sabba_Ab_name_lg7,position=sabba_Ab_loci_lg7)
sabba_ab_lg7<-data.frame(marker=sabba_ab_name_lg7,position=sabba_Ab_loci_lg7)
sabba_ab_lg8<-data.frame(marker=sabba_Ab_name_lg8,position=sabba_Ab_loci_lg8)
sabba_Ab_loci_lg5<-sabba_ab_loci[39:44]
sabba_Ab_name_lg5<-sabba_ab_name[39:44]
sabba_Ab_loci_lg1<-sabba_ab_loci[2:4]
sabba_Ab_name_lg1<-sabba_ab_name[2:4]
sabba_ab_lg5<-data.frame(marker=sabba_Ab_name_lg5,position=sabba_Ab_loci_lg5)
sabba_ab_lg1<-data.frame(marker=sabba_Ab_name_lg1,position=sabba_Ab_loci_lg1)
list_lg1<-list(arya_lg1,kotta_lg1,cobos_lg1,sabba_fw_lg1,taran_lg1,anupama_lg1,tosh_lg1,daba_lg1,palomino_lg1,santra_lg1,patil_lg1,winter_lg1,galvez_lg1,sabba_ab_lg1)
LPmerge::LPmerge(Maps = list_lg1)
kotta_lg1
cobos_lg1
sabba_ab_lg1
sabba_fw_lg1
list_lg1
winter_name_lg1<-winter_name[2:40]
winter_loci_lg1<-winter_loci[2:40]
winter_lg1<-data.frame(marker=winter_name_lg1,position=winter_loci_lg1)
list_lg1<-list(arya_lg1,kotta_lg1,cobos_lg1,sabba_fw_lg1,taran_lg1,anupama_lg1,tosh_lg1,daba_lg1,palomino_lg1,santra_lg1,patil_lg1,winter_lg1,galvez_lg1,sabba_ab_lg1)
LPmerge::LPmerge(Maps = list_lg1)
patil_name<-map_all$Patil.et.al..
patil_name_lg1<-patil_name[2:3]
patil_name_lg2<-patil_name[6:13]
patil_name_lg3<-patil_name[16:21]
patil_name_lg4<-patil_name[24:27]
patil_name_lg5<-patil_name[30:32]
patil_lg1<-data.frame(marker=patil_name_lg1,position=patil_loci_lg1)
patil_lg2<-data.frame(marker=patil_name_lg2,position=patil_loci_lg2)
patil_lg3<-data.frame(marker=patil_name_lg3,position=patil_loci_lg3)
patil_lg4<-data.frame(marker=patil_name_lg4,position=patil_loci_lg4)
patil_lg5<-data.frame(marker=patil_name_lg5,position=patil_loci_lg5)
patil_lg6<-data.frame(marker=patil_name_lg6,position=patil_loci_lg6)
list_lg1<-list(arya_lg1,kotta_lg1,cobos_lg1,sabba_fw_lg1,taran_lg1,anupama_lg1,tosh_lg1,daba_lg1,palomino_lg1,santra_lg1,patil_lg1,winter_lg1,galvez_lg1,sabba_ab_lg1)
list_lg1
list_lg1<-list(arya_lg1,kotta_lg1,cobos_lg1,sabba_fw_lg1,taran_lg1,anupama_lg1,tosh_lg1,palomino_lg1,santra_lg1,patil_lg1,winter_lg1,galvez_lg1,sabba_ab_lg1)
LPmerge::LPmerge(Maps = list_lg1)
LPmerge::LPmerge(Maps = list_lg1)
list_lg1<-list(arya_lg1,kotta_lg1,cobos_lg1,sabba_fw_lg1,taran_lg1,anupama_lg1,tosh_lg1,palomino_lg1,santra_lg1,patil_lg1,winter_lg1,galvez_lg1,sabba_ab_lg1)
list_lg1
LPmerge::LPmerge(maps=list_lg1)
LPmerge::LPmerge(Maps = list_lg1\)
LPmerge::LPmerge(Maps = list_lg1)
LPmerge::LPmerge(Maps = list_lg1)
savehistory("C:/Users/ishit/OneDrive/Documents/Chickpea/history_new.Rproj")
save.image("C:/Users/ishit/OneDrive/Documents/Chickpea/consensus_lg1.RData")
save.image("C:/Users/ishit/OneDrive/Documents/Chickpea/consensus_lg1.RData")
list_lg2<-list(kotta_loci_lg2,sabba_ab_lg2,sabba_fw_lg2,arya_loci_lg2,tosh_lg2,anupama_lg2,taran_lg2,palomino_lg2,iruela_lg2,muehlbauer_lg2,halila_lg2,gowda_lg2,santra_lg2,patil_lg2,winter_lg2,galvez_lg2)
LPmerge::LPmerge(Maps = list_lg2)
list_lg2
list_lg2<-list(sabba_ab_lg2,sabba_fw_lg2,tosh_lg2,anupama_lg2,taran_lg2,palomino_lg2,iruela_lg2,muehlbauer_lg2,halila_lg2,gowda_lg2,santra_lg2,patil_lg2,winter_lg2,galvez_lg2)
LPmerge::LPmerge(Maps = list_lg2)
kotta_lg2<-data.frame(marker=kotta_name_lg2,position=kotta_loci_lg2)
kotta_name_lg2
kotta_loci_lg2
kotta_loci_lg1<-kotta_loci[2:10]
kotta_loci_lg2<-kotta_loci[13:28
kotta_loci_lg2<-kotta_loci[13:28
kotta_loci_lg2<-kotta_loci[13:28]
kotta_loci_lg3<-kotta_loci[30:39]
kotta_loci_lg5a<-kotta_loci[55:61]
kotta_loci_lg5b<-kotta_loci[64:67]
kotta_loci_lg6<-kotta_loci[70:83]
kotta_loci_lg7<-kotta_loci[86:93]
kotta_loci_lg8a<-kotta_loci[96:99]
kotta_loci_lg8b<-kotta_loci[102:103]
kotta_loci_lg4<-kotta_loci[42:52]
kotta_name_lg1<-kotta_name[2:10]
kotta_name_lg2<-kotta_name[13:28]
kotta_name_lg3<-kotta_name[30:39]
kotta_name_lg4<-kotta_name[42:52]
kotta_name_lg5a<-kotta_name[55:61]
kotta_name_lg5b<-kotta_name[64:67]
kotta_name_lg6<-kotta_name[70:83]
kotta_name_lg7<-kotta_name[86:93]
kotta_name_lg8a<-kotta_name[96:99]
kotta_name_lg8b<-kotta_name[102:103]
arya_lg2<-data.frame(marker=arya_name_lg2,position=arya_loci_lg2)
arya_lg3<-data.frame(marker=arya_name_lg3,position=arya_loci_lg3)
arya_lg4<-data.frame(marker=arya_name_lg4,position=arya_loci_lg4)
arya_lg5<-data.frame(marker=arya_name_lg5,position=arya_loci_lg5)
arya_lg6<-data.frame(marker=arya_name_lg6,position=arya_loci_lg6)
arya_lg7<-data.frame(marker=arya_name_lg7,position=arya_loci_lg7)
arya_lg8<-data.frame(marker=arya_name_lg8,position=arya_loci_lg7)
arya_lg8<-data.frame(marker=arya_name_lg8,position=arya_loci_lg8)
list_lg2<-list(kotta_lg2,sabba_ab_lg2,sabba_fw_lg2,arya_lg2,tosh_lg2,anupama_lg2,taran_lg2,palomino_lg2,iruela_lg2,muehlbauer_lg2,halila_lg2,gowda_lg2,santra_lg2,patil_lg2,winter_lg2,galvez_lg2)
kotta_lg2<-data.frame(marker=kotta_name_lg2,position=kotta_loci_lg2)
kotta_lg3<-data.frame(marker=kotta_name_lg3,position=kotta_loci_lg3)
kotta_lg3<-data.frame(marker=kotta_name_lg3,position=kotta_loci_lg3)
kotta_lg4<-data.frame(marker=kotta_name_lg4,position=kotta_loci_lg4)
kotta_lg5a<-data.frame(marker=kotta_name_lg5a,position=kotta_loci_lg5a)
kotta_lg5b<-data.frame(marker=kotta_name_lg5b,position=kotta_loci_lg5b)
kotta_lg6<-data.frame(marker=kotta_name_lg6,position=kotta_loci_lg6)
kotta_lg7<-data.frame(marker=kotta_name_lg7,position=kotta_loci_lg7)
kotta_lg8a<-data.frame(marker=kotta_name_lg8a,position=kotta_loci_lg8a)
kotta_lg8b<-data.frame(marker=kotta_name_lg8b,position=kotta_loci_lg8b)
list_lg2<-list(kotta_lg2,sabba_ab_lg2,sabba_fw_lg2,arya_lg2,tosh_lg2,anupama_lg2,taran_lg2,palomino_lg2,iruela_lg2,muehlbauer_lg2,halila_lg2,gowda_lg2,santra_lg2,patil_lg2,winter_lg2,galvez_lg2)
LPmerge::LPmerge(Maps = list_lg2)
list_lg2<-list(sabba_ab_lg2,sabba_fw_lg2,tosh_lg2,anupama_lg2,taran_lg2,palomino_lg2,iruela_lg2,muehlbauer_lg2,halila_lg2,gowda_lg2,santra_lg2,patil_lg2,winter_lg2,galvez_lg2)
LPmerge::LPmerge(Maps = list_lg2)
cons_lg2_all<-LPmerge::LPmerge(Maps = list_lg2)
View(cons_lg2_all)
cons_lg2_all[[1]]
fix(cons_lg2_all)
list_lg2<-list(kotta_lg2,arya_lg2,sabba_ab_lg2,sabba_fw_lg2,tosh_lg2,anupama_lg2,palomino_lg2,irulena_lg2,muehlbauer_lg2,halila_lg2,winter_lg2,galvez_lg2,patil_lg2,santra_lg2)
list_lg2
LPmerge::LPmerge(Maps = list_lg2)
kotta_lg2<-data.frame(marker=kotta_name_lg2,position=kotta_loci_lg2)
kotta_lg2
kotta_name_lg2<-kotta_name[13:28]
kotta_loci_lg2<-kotta_loci[13:28]
kotta_lg2<-data.frame(marker=kotta_name_lg2,position=kotta_loci_lg2)
kotta_lg2
kotta_loci_lg2<-kotta_loci[13:27]
kotta_name_lg2<-kotta_name[13:27]
kotta_lg2<-data.frame(marker=kotta_name_lg2,position=kotta_loci_lg2)
kotta_lg2
list_lg2<-list(kotta_lg2,arya_lg2,sabba_ab_lg2,sabba_fw_lg2,tosh_lg2,anupama_lg2,palomino_lg2,irulena_lg2,muehlbauer_lg2,halila_lg2,winter_lg2,galvez_lg2,patil_lg2,santra_lg2)
LPmerge::LPmerge(Maps = list_lg2)
consensus_lg2<-LPmerge::LPmerge(Maps = list_lg2)
list_lg3<-list(arya_lg3,kotta_lg3,sabba_ab_lg3,sabba_fw_lg3,tosh_lg3,palomino_lg3,anupama_lg3,anupama_lg3b,anuradha_lg3,taran_lg3,santra_lg3,patil_lg3,winter_lg3,galvez_lg3)
list_lg3<-list(arya_lg3,kotta_lg3,sabba_ab_lg3,sabba_fw_lg3,tosh_lg3,palomino_lg3,anupama_lg3a,anupama_lg3b,anuradha_lg3,taran_lg3,santra_lg3,patil_lg3,winter_lg3,galvez_lg3)
LPmerge::LPmerge(Maps = list_lg3)
list_lg3<-list(arya_lg3,kotta_lg3,sabba_ab_lg3,sabba_fw_lg3,tosh_lg3,palomino_lg3,anupama_lg3a,anupama_lg3b,anuradha_lg3,santra_lg3,patil_lg3,winter_lg3,galvez_lg3)
LPmerge::LPmerge(Maps = list_lg3)
LPmerge::LPmerge(Maps = list_lg3)
list_lg3
tosh_loci_lg3<-tosh_loci[45:57]
tosh_name_lg3<-tosh_name[45:57]
sabba_fw_name_lg3<-sabba_fw_name[20:26]
sabba_fw_name_lg3
sabba_lg3<-data.frame(marker=sabba_fw_name_lg3,position=sabba_fw_loci_lg3)
list_lg3<-list(arya_lg3,kotta_lg3,sabba_ab_lg3,sabba_fw_lg3,tosh_lg3,palomino_lg3,anupama_lg3a,anupama_lg3b,anuradha_lg3,santra_lg3,patil_lg3,winter_lg3,galvez_lg3)
LPmerge::LPmerge(Maps = list_lg3)
list_lg3
savehistory("C:/Users/ishit/OneDrive/Documents/Chickpea/consen_14.Rproj")