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replace repeated id in a pedigree list
2 messages · Roberta Carriero, Rui Barradas
Hello,
Ok, try the following.
fun <- function(x, d, last){
new <- last
if(any(d)){
ii <- which(d)
for(i in ii){
new <- new + 1
old <- x$ID[i]
x$ID[i] <- new
x$FA_ID[x$FA_ID == old] <- new
x$MO_ID[x$MO_ID == old] <- new
}
} else new <- FALSE
list(new = new, DF = x)
}
lastid <- nrow(dat)
idx <- duplicated(dat$ID)
sp <- split(dat, dat$FAMID)
dup <- split(idx, dat$FAMID)
result <- vector("list", length(sp))
for(i in seq_along(sp)){
ret <- fun(sp[[i]], dup[[i]], lastid)
result[[i]] <- ret$DF
if(ret$new) lastid <- ret$new
}
d2 <- do.call(rbind, result)
# check (should be zero)
sum(duplicated(d2$ID))
Hope this helps,
Rui Barradas
Em 30-10-2012 11:22, Roberta Carriero escreveu:
From: robertacar at hotmail.it To: smartpink111 at yahoo.com Subject: RE: [R] replace repeated id in a pedigree list Date: Tue, 30 Oct 2012 09:51:50 +0100 You are right! I want to "replace the second 6 with a new ID". For example I have id 6 which is repeated 2 times. In family 1 it appears one time. In family 37 I should replace id 6 with a new id whenever it appears, not only as founder but also as father. It is important to use a new id which doesn't exist in all the pedigrees belonging to the "Pedigree.txt" file. Thank you for help RegardsRoberta FAMID ID FA ID MO ID SEX STATUS> 1 1 0 0 2 0> 1 2 3 1 2 2> 1 4 3 1 1 2> 1 5 3 1 1 0> 1 6 3 1 1 0> 1 7 3 1 2 2> 1 8 3 1 1 0> 1 9 3 1 1 0> 1 10 3 1 2 0> 1 11 3 1 1 0> 1 3 0 0 1 0 37 277 0 0 2 0> 37 546 547 548 2 2> 37 549 547 548 1 2> 37 550 6 551 1 0> 37 551 552 553 2 2> 37 552 554 555 1 0> 37 556 0 0 2 0> 37 557 6 551 2 0> 37 558 6 551 2 2> 37 559 6 551 1 0> 37 560 6 551 1 2> 37 6 0 0 1 0> 37 554 0 0 1 0> 37 561 554 562 1 0> 37 562 0 0 2 0> 37 555 0 0 2 0> 37 563 521 558 1 0> 37 306 0 0 1 0> 37 521 306 307 1 2> 37 564 521 558 2 2> 37 565 521 558 1 2> 37 307 0 0 2 2> 37 566 6 551 1 0> 37 548 6 551 2 2> 37 567 6 551 2 2> 37 568 561 556 1 0> 37 547 568 277 1 0> 37 553 0 0 2 0> Date: Mon, 29 Oct 2012 20:23:56 -0700
From: smartpink111 at yahoo.com
Subject: Re: [R] replace repeated id in a pedigree list
To: robertacar at hotmail.it
Hi,
I am a bit confused by this statement
"I want to replace repeated individual identifiers with new id and to
replace them not only in id column but also in father and mother id
columns"
In the dataset, you have repeated identifiers for ID, FAID and MOID.
For eg.
source("Pedigree.txt")
head(dat1)
# FAMID ID FAID MOID SEX STATUS
#1 1 1 0 0 2 0
#2 1 2 3 1 2 2
#3 1 4 3 1 1 2
#4 1 5 3 1 1 0
#5 1 6 3 1 1 0
#6 1 7 3 1 2 2
dat2<-dat1[duplicated(dat1$ID)|duplicated(dat1$ID,fromLast=TRUE),]
dat3<-dat2[order(dat2$ID),]
head(dat3)
# FAMID ID FAID MOID SEX STATUS
#5 1 6 3 1 1 0
#603 37 6 0 0 1 0
#17 2 20 0 0 1 0
#469 29 20 0 0 1 0
#21 2 24 12 16 1 0
#533 32 24 0 0 1 0
dat1$ID[duplicated(dat1$ID)|duplicated(dat1$ID,fromLast=TRUE)]
# [1] 6 20 24 29 30 31 47 62 63 95 96 99 100 93 101 102 83 105
#[19] 107 112 113 115 117 108 142 155 146 157 161 96 167 177 105 107 192 108
#[37] 203 204 113 212 221 228 229 107 236 239 223 155 146 251 157 258 260 257
#[55] 256 277 279 212 260 83 288 296 251 294 306 303 307 296 328 339 328 342
#[73] 333 338 345 258 177 257 192 256 382 378 377 167 404 410 203 204 413 113
#[91] 422 115 426 427 117 411 412 434 435 20 29 449 30 31 450 404 464 479
#[109] 480 481 413 483 484 434 476 477 47 288 24 506 500 501 339 328 516 294
#[127] 306 521 303 333 307 516 306 543 545 307 277 6 306 521 307 112 506 500
#[145] 501 596 598 599 598 62 63 229 236 239 627 619 620 599 638 645 650 651
#[163] 643 642 646 653 95 99 100 663 93 101 638 674 464 411 645 650 671 412
#[181] 651 672 646 696 686 685 411 671 378 377 412 672 653 733 435 760 650 651
#[199] 643 642 686 102 685 221 228 101 223 480 142 481 382 733 596 161 476 477
#[217] 696 627 674 760 645 650 651 619 646 620 239 410 422 426 427 479 483 484
#[235] 663 29 449 545 31 450 279 177 342 943 947 192 949 338 345 945 944 177
#[253] 543 943 947 192 949 945 944 410 333 427
#The same way you can get the repeated FAID and MOID
dat1$FAID[duplicated(dat1$FAID)|duplicated(dat1$FAID,fromLast=TRUE)]
dat1$MOID[duplicated(dat1$MOID)|duplicated(dat1$MOID,fromLast=TRUE)]
From the dat3 IDs, you have 6 repeated 2 times. In that case, you want to replace the second 6 with a new ID. Regarding the new ID, will it work if that ID is already present in FAID or MOID?
A.K.
----- Original Message -----
From: Roberta Carriero <robertacar at hotmail.it>
To: r-help at r-project.org
Cc:
Sent: Monday, October 29, 2012 2:08 PM
Subject: [R] replace repeated id in a pedigree list
Hello,
I have a pedigree file such this:
FAMID ID FA ID MO ID SEX STATUS
1 1 0 0 2 0
1 2 3 1 2 2
1 4 3 1 1 2
1 5 3 1 1 0
1 6 3 1 1 0
1 7 3 1 2 2
1 8 3 1 1 0
1 9 3 1 1 0
1 10 3 1 2 0
1 11 3 1 1 0
1 3 0 0 1 0
2 12 13 14 1 0
2 15 12 16 2 0
2 17 12 16 1 0
2 18 12 16 1 0
2 19 12 16 1 0
2 20 0 0 1 0
2 21 0 0 2 0
2 22 12 16 2 2
2 23 12 16 1 0
2 24 12 16 1 0
2 25 12 16 1 0
2 26 12 16 2 0
2 27 28 21 2 2
2 29 0 0 2 0
2 14 0 0 2 0
2 30 31 29 2 0
2 13 31 29 1 0
2 31 0 0 1 0
2 28 20 30 1 0
2 32 28 21 2 2
2 16 0 0 2 0
3 33 34 35 2 0
3 35 0 0 2 0
3 36 34 35 1 0
3 37 34 35 1 0
3 38 34 35 2 0
3 39 34 35 1 0
3 40 34 35 2 0
3 41 34 35 2 0
3 42 34 35 2 2
3 43 34 35 1 0
3 34 0 0 1 0
3 44 34 35 2 0
3 45 34 35 1 2
4 46 47 48 2 2
4 49 47 48 1 0
4 50 47 48 1 0
4 51 47 48 2 0
4 47 0 0 1 0
4 52 47 48 1 2
4 53 47 48 2 2
4 48 0 0 2 2
4 54 47 48 2 2
4 55 47 48 2 2
5 56 57 58 1 0
5 59 60 61 2 2
5 60 62 63 1 2
5 62 0 0 1 0
5 63 0 0 2 2
5 57 0 0 1 0
5 64 57 58 1 0
5 65 60 61 2 2
5 66 57 58 1 0
5 67 68 69 2 2
5 70 68 69 1 0
5 71 68 69 2 2
5 68 0 0 1 0
5 72 57 58 1 0
5 61 57 58 2 2
5 73 57 58 1 0
5 74 57 58 2 0
5 75 60 61 2 2
5 76 57 58 1 0
5 69 57 58 2 2
5 77 57 58 2 2
5 78 0 0 1 0
5 58 0 0 2 0
5 79 78 77 2 2
5 80 78 77 2 2
5 81 78 77 1 0
6 82 83 84 1 0
6 85 83 84 1 0
6 86 0 0 1 2
6 87 86 88 1 0
6 89 86 88 1 0
6 90 86 88 2 0
6 91 86 88 2 2
6 92 87 93 2 2
6 94 86 88 2 2
6 84 0 0 2 0
6 95 0 0 2 0
6 96 83 84 1 0
6 97 83 84 1 0
6 98 83 84 2 0
6 99 0 0 1 2
6 100 99 95 2 0
6 93 101 100 2 0
6 101 0 0 1 0
6 102 83 84 2 0
6 88 83 84 2 2
6 83 0 0 1 0
6 103 83 84 1 0
7 104 105 106 1 0
7 105 107 108 1 0
7 107 0 0 1 0
7 109 105 106 2 2
7 110 111 112 1 0
7 112 0 0 2 2
7 113 0 0 2 2
7 114 115 116 1 2
7 115 117 113 1 0
7 118 115 116 1 2
7 119 115 116 1 0
7 117 0 0 1 2
7 108 0 0 2 2
7 116 111 112 2 2
7 120 111 112 1 0
7 106 111 112 2 2
7 111 0 0 1 0
7 121 105 106 2 2
8 122 123 124 2 0
8 125 123 124 1 0
8 126 123 124 1 0
8 127 123 124 1 0
8 128 123 124 1 2
8 129 123 124 1 0
8 130 123 124 1 0
8 131 123 124 2 0
8 123 0 0 1 0
8 124 0 0 2 0
8 132 123 124 2 2
9 133 134 135 2 0
9 136 137 133 1 0
9 138 137 133 2 0
9 137 139 140 1 0
9 141 139 140 1 0
9 142 0 0 1 0
9 143 137 133 2 2
9 144 145 146 2 2
9 145 147 148 1 0
9 149 145 146 2 0
9 150 145 146 2 0
9 151 137 133 2 0
9 152 137 133 1 0
9 153 137 133 1 2
9 148 0 0 2 0
9 154 137 133 1 0
9 155 141 156 2 0
9 146 157 155 2 0
9 157 0 0 1 0
9 158 145 146 1 0
9 159 145 146 1 0
9 160 0 0 1 0
9 161 160 162 2 0
9 135 160 162 2 0
9 134 0 0 1 0
9 162 0 0 2 0
9 140 0 0 2 0
9 139 0 0 1 0
9 156 0 0 2 0
9 147 142 161 1 0
10 163 96 164 2 2
10 165 96 164 1 2
10 164 166 167 2 2
10 168 166 167 1 0
10 169 166 167 1 0
10 166 0 0 1 0
10 170 166 167 2 0
10 96 0 0 1 0
10 171 96 164 2 2
10 167 0 0 2 2
10 172 166 167 2 0
10 173 166 167 1 0
10 174 166 167 2 0
11 175 0 0 2 0
11 176 107 108 2 0
11 177 0 0 2 0
11 178 107 108 2 2
11 179 180 181 1 0
11 182 183 178 2 0
11 184 107 108 1 0
11 185 183 178 1 2
11 186 180 181 2 2
11 187 180 181 1 2
11 183 180 181 1 2
11 188 183 178 2 2
11 105 107 108 1 0
11 107 0 0 1 0
11 189 0 0 2 0
11 190 0 0 2 0
11 191 107 108 1 0
11 192 193 189 1 0
11 194 193 189 1 0
11 193 0 0 1 0
11 108 195 175 2 2
11 196 180 181 1 0
11 197 180 181 1 0
11 198 180 181 1 0
11 199 180 181 2 0
11 180 0 0 1 0
11 195 192 177 1 0
11 181 194 190 2 0
12 200 201 202 1 0
12 203 0 0 2 0
12 204 0 0 1 0
12 205 201 202 2 2
12 201 0 0 1 0
12 206 204 203 2 0
12 207 204 203 1 0
12 202 204 203 2 2
12 113 204 203 2 2
12 208 204 203 2 0
12 209 204 203 1 0
12 210 204 203 1 0
13 211 212 213 2 0
13 213 0 0 2 0
13 214 212 213 1 2
13 212 0 0 1 0
13 215 212 213 1 0
13 216 212 213 2 2
13 217 212 213 1 0
13 218 212 213 2 0
13 219 212 213 1 0
13 220 212 213 1 0
14 221 0 0 2 0
14 222 223 221 1 0
14 224 223 221 1 0
14 225 223 221 1 0
14 226 223 221 1 0
14 227 223 221 2 0
14 228 223 221 2 0
14 229 0 0 2 0
14 230 0 0 2 2
14 231 223 221 2 0
14 232 233 230 1 2
14 234 233 230 1 0
14 107 223 221 1 0
14 235 234 236 2 2
14 237 233 230 1 2
14 238 234 236 1 0
14 236 239 229 2 0
14 239 0 0 1 2
14 240 223 221 1 0
14 241 233 230 1 0
14 233 223 221 1 2
14 223 0 0 1 0
15 242 157 155 2 0
15 243 157 155 2 0
15 244 245 246 1 2
15 247 245 246 1 2
15 248 157 155 1 0
15 249 157 155 1 0
15 155 0 0 2 0
15 250 157 155 2 0
15 146 157 155 2 0
15 251 157 155 1 2
15 157 0 0 1 0
15 246 157 155 2 2
15 252 157 155 2 0
15 253 245 246 1 0
15 254 245 246 1 0
15 245 0 0 1 0
16 255 256 257 2 0
16 258 256 257 2 0
16 259 256 257 2 0
16 260 256 257 1 0
16 261 256 257 2 2
16 262 256 257 1 0
16 263 256 257 1 0
16 264 256 257 1 0
16 265 256 257 1 0
16 266 256 257 2 0
16 267 0 0 2 2
16 257 0 0 2 0
16 268 0 0 1 0
16 269 270 267 1 2
16 270 268 261 1 2
16 271 268 261 1 0
16 256 0 0 1 0
16 272 270 267 2 2
17 273 274 275 1 0
17 276 274 275 2 0
17 277 274 275 2 0
17 278 274 275 2 0
17 279 274 275 2 0
17 212 274 275 1 0
17 280 260 281 2 2
17 260 0 0 1 0
17 281 274 275 2 2
17 275 0 0 2 0
17 83 274 275 1 0
17 282 260 281 2 2
17 274 0 0 1 0
18 283 284 285 1 0
18 286 284 285 1 0
18 285 0 0 2 0
18 284 0 0 1 0
18 287 284 285 1 2
18 288 284 285 2 2
18 289 284 285 1 0
18 290 284 285 2 0
18 291 284 285 2 0
19 292 293 294 1 0
19 293 0 0 1 2
19 295 296 297 2 2
19 298 293 294 1 0
19 299 296 297 1 2
19 297 293 294 2 2
19 300 293 294 1 0
19 296 0 0 1 2
19 301 296 297 2 2
19 302 251 303 2 2
19 251 0 0 1 2
19 304 251 303 1 2
19 305 251 303 1 2
19 294 306 307 2 2
19 306 0 0 1 0
19 303 306 307 2 2
19 307 0 0 2 2
20 308 309 310 2 2
20 310 0 0 2 0
20 311 309 310 1 2
20 312 309 310 1 0
20 296 309 310 1 2
20 313 309 310 2 2
20 309 0 0 1 0
20 314 315 313 2 2
20 316 315 313 1 2
20 315 0 0 1 0
20 317 309 310 1 0
21 318 319 320 2 2
21 319 0 0 1 0
21 320 0 0 2 2
22 321 322 323 2 0
22 324 322 323 2 0
22 325 322 323 1 2
22 326 322 323 2 2
22 327 322 323 1 2
22 328 322 323 1 0
22 329 322 323 2 0
22 330 322 323 2 2
22 331 322 323 1 0
22 322 0 0 1 0
22 323 0 0 2 0
23 332 328 333 2 0
23 334 328 333 1 0
23 335 328 333 1 0
23 336 337 338 2 2
23 339 328 333 2 2
23 340 328 333 1 2
23 341 328 333 1 2
23 337 328 333 1 2
23 328 0 0 1 0
23 342 0 0 2 2
23 343 337 338 1 2
23 344 328 333 1 0
23 333 0 0 2 2
23 338 345 342 2 2
23 345 0 0 1 0
24 346 347 348 1 0
24 349 347 348 1 0
24 350 347 348 2 0
24 351 347 348 1 0
24 352 347 348 2 0
24 347 0 0 1 0
24 258 256 257 2 0
24 353 347 348 2 0
24 177 354 355 2 0
24 356 357 358 1 0
24 357 359 360 1 2
24 361 359 360 1 0
24 362 357 358 1 2
24 359 363 258 1 2
24 364 359 360 1 2
24 365 359 360 1 2
24 366 359 360 2 2
24 367 347 348 2 2
24 368 347 348 1 0
24 369 347 348 1 0
24 370 347 348 2 0
24 371 357 358 2 2
24 360 0 0 2 2
24 358 0 0 2 2
24 257 354 355 2 0
24 354 0 0 1 0
24 355 0 0 2 0
24 192 0 0 1 0
24 256 0 0 1 0
24 372 359 360 2 0
24 363 0 0 1 0
24 348 192 177 2 0
25 373 374 375 2 0
25 376 377 378 2 0
25 379 380 376 2 2
25 375 0 0 2 0
25 380 0 0 1 0
25 381 380 376 2 2
25 382 0 0 1 0
25 383 384 385 1 2
25 386 382 387 2 2
25 388 382 387 2 0
25 384 382 387 1 2
25 389 382 387 1 0
25 390 380 376 1 0
25 391 392 381 1 0
25 393 0 0 2 0
25 385 392 381 2 2
25 392 394 373 1 0
25 395 0 0 1 0
25 378 0 0 2 0
25 377 395 393 1 0
25 374 395 393 1 0
25 387 0 0 2 0
25 396 380 376 2 2
25 397 380 376 1 0
25 398 380 376 2 2
25 394 0 0 1 0
26 399 400 401 2 0
26 167 400 401 2 2
26 402 400 401 2 2
26 403 400 401 1 0
26 404 400 401 1 2
26 405 400 401 2 0
26 401 0 0 2 0
26 400 0 0 1 0
27 406 407 408 1 0
27 409 407 408 1 0
27 410 0 0 2 0
27 203 0 0 2 0
27 204 411 412 1 0
27 413 0 0 2 2
27 414 415 416 2 0
27 407 0 0 1 0
27 417 407 408 2 2
27 418 407 408 1 2
27 419 407 408 1 2
27 420 419 413 1 2
27 421 419 413 2 0
27 113 204 203 2 2
27 422 0 0 2 0
27 408 423 424 2 0
27 115 117 113 1 0
27 425 415 416 1 2
27 426 0 0 1 0
27 423 426 422 1 0
27 427 426 422 1 0
27 415 117 113 1 2
27 428 117 113 1 0
27 117 427 410 1 2
27 411 0 0 1 0
27 429 0 0 1 0
27 430 411 412 2 0
27 412 0 0 2 0
27 416 431 417 2 2
27 431 0 0 1 2
27 432 117 113 2 0
27 424 429 430 2 0
28 433 434 435 2 0
28 436 434 435 1 2
28 434 0 0 1 2
28 435 0 0 2 2
29 437 438 439 1 0
29 440 0 0 1 0
29 441 440 442 2 2
29 443 440 442 1 2
29 444 440 442 1 0
29 445 440 442 2 0
29 20 0 0 1 0
29 442 438 439 2 2
29 438 446 447 1 0
29 448 440 442 1 0
29 447 0 0 2 0
29 29 0 0 2 0
29 449 0 0 2 0
29 30 31 29 2 0
29 31 450 449 1 0
29 446 450 449 1 0
29 450 0 0 1 0
29 439 20 30 2 0
30 451 404 452 2 0
30 453 404 452 1 0
30 454 404 452 2 0
30 455 404 452 1 0
30 456 457 458 1 2
30 459 457 458 1 2
30 457 404 452 1 2
30 460 404 452 1 0
30 404 0 0 1 2
30 461 404 452 2 0
30 462 463 464 1 2
30 465 463 464 2 0
30 466 404 452 1 0
30 464 0 0 2 2
30 458 463 464 2 2
30 463 0 0 1 0
30 452 0 0 2 2
30 467 463 464 1 0
30 468 463 464 1 0
31 469 0 0 1 0
31 470 469 471 2 0
31 472 469 471 1 0
31 473 469 471 2 0
31 474 469 471 1 0
31 471 0 0 2 0
31 475 476 477 1 0
31 478 476 477 2 2
31 479 476 477 2 2
31 480 476 477 1 2
31 481 476 477 2 2
31 482 476 477 2 2
31 413 476 477 2 2
31 483 484 479 2 2
31 485 469 471 1 2
31 484 469 471 1 2
31 434 469 471 1 2
31 486 484 479 2 2
31 487 469 471 1 0
31 476 0 0 1 0
31 477 0 0 2 0
32 488 489 490 1 0
32 490 0 0 2 0
32 489 0 0 1 0
32 491 489 490 1 2
32 492 493 494 2 2
32 493 0 0 1 0
32 47 489 490 1 0
32 494 489 490 2 2
32 288 0 0 2 2
32 495 24 288 1 2
32 496 24 288 1 0
32 497 24 288 1 2
32 24 0 0 1 0
32 498 497 492 2 2
33 499 500 501 1 0
33 502 500 501 2 2
33 503 500 501 1 0
33 504 500 501 2 2
33 505 500 501 2 2
33 506 500 501 1 0
33 500 0 0 1 0
33 501 0 0 2 0
34 507 306 307 1 0
34 508 306 307 1 0
34 509 306 307 2 0
34 510 511 512 2 2
34 511 0 0 1 2
34 513 511 512 1 2
34 514 511 512 1 2
34 339 328 333 2 2
34 328 0 0 1 0
34 515 306 307 1 0
34 516 306 307 1 2
34 517 306 307 1 0
34 518 519 339 1 0
34 294 306 307 2 2
34 306 0 0 1 0
34 520 519 339 1 2
34 521 306 307 1 2
34 512 306 307 2 2
34 522 519 339 2 2
34 523 519 339 1 0
34 519 306 307 1 2
34 524 519 339 1 2
34 303 306 307 2 2
34 333 0 0 2 2
34 307 0 0 2 2
35 525 0 0 1 2
35 526 525 527 1 2
35 528 525 527 1 0
35 527 0 0 2 2
36 529 0 0 2 2
36 530 0 0 1 2
36 531 530 532 1 0
36 533 530 532 1 2
36 534 530 532 1 0
36 535 530 532 1 2
36 536 530 532 2 2
36 532 537 529 2 2
36 538 537 529 2 2
36 537 0 0 1 2
36 516 306 307 1 2
36 539 540 536 1 2
36 541 516 538 2 2
36 306 0 0 1 0
36 542 516 538 1 2
36 543 0 0 1 2
36 544 543 545 2 2
36 540 543 545 1 2
36 545 0 0 2 2
36 307 0 0 2 2
38 569 570 571 2 0
38 572 570 571 1 0
38 573 570 571 2 0
38 570 0 0 1 0
38 574 570 571 2 0
38 575 570 571 1 0
38 112 570 571 2 2
38 576 570 571 2 2
38 571 0 0 2 0
39 577 578 579 2 0
39 580 578 579 1 0
39 581 578 579 1 2
39 582 578 579 2 0
39 578 583 584 1 0
39 585 0 0 1 0
39 579 0 0 2 0
39 506 500 501 1 0
39 586 578 579 2 2
39 587 506 586 2 2
39 588 578 579 2 2
39 500 585 589 1 0
39 583 585 589 1 0
39 589 0 0 2 0
39 584 0 0 2 0
39 501 0 0 2 0
40 590 591 592 1 0
40 593 591 592 2 0
40 594 591 592 1 0
40 595 591 592 1 2
40 596 591 592 1 2
40 591 0 0 1 0
40 592 0 0 2 0
41 597 598 599 2 0
41 600 598 599 2 0
41 601 598 599 2 0
41 598 0 0 1 0
41 602 598 599 1 0
41 603 598 599 1 2
41 604 598 599 2 0
41 599 0 0 2 2
42 605 606 607 2 0
42 608 606 607 1 2
42 609 606 607 2 0
42 610 606 607 2 0
42 607 0 0 2 0
42 598 606 607 1 0
42 611 606 607 1 0
42 612 606 607 2 2
42 606 0 0 1 0
43 613 62 63 1 2
43 614 613 615 1 2
43 62 0 0 1 0
43 63 0 0 2 2
43 229 0 0 2 0
43 616 613 615 2 2
43 236 239 229 2 0
43 239 0 0 1 2
43 615 239 229 2 2
43 617 239 229 2 2
44 618 619 620 1 2
44 621 619 620 1 0
44 622 619 620 1 0
44 623 0 0 2 0
44 624 618 623 2 2
44 625 618 623 1 0
44 626 618 623 2 0
44 627 619 620 2 0
44 628 619 620 1 2
44 629 619 620 2 2
44 630 618 623 1 0
44 631 618 623 1 0
44 632 619 620 2 2
44 633 618 623 2 0
44 634 618 623 1 0
44 619 0 0 1 0
44 620 0 0 2 0
45 635 636 637 1 0
45 599 638 639 2 2
45 640 638 639 1 0
45 637 638 639 2 2
45 641 636 637 2 2
45 636 642 643 1 2
45 644 636 637 1 2
45 638 645 646 1 0
45 647 636 637 1 2
45 648 636 637 1 2
45 649 636 637 1 2
45 645 0 0 1 0
45 650 0 0 1 0
45 651 0 0 2 0
45 643 0 0 2 0
45 639 0 0 2 0
45 642 650 651 1 0
45 646 650 651 2 0
46 652 653 654 2 2
46 655 653 654 2 0
46 656 653 654 2 2
46 657 653 654 1 0
46 654 0 0 2 0
46 653 0 0 1 0
47 95 0 0 2 0
47 658 101 100 2 0
47 99 659 660 1 2
47 100 99 95 2 0
47 661 659 660 1 0
47 662 659 660 1 2
47 663 659 660 2 2
47 664 659 660 2 2
47 665 101 100 2 0
47 666 101 100 1 0
47 93 101 100 2 0
47 667 101 100 2 2
47 101 0 0 1 0
47 660 0 0 2 0
47 659 0 0 1 0
48 668 645 646 2 0
48 669 645 646 1 2
48 670 671 672 2 0
48 673 669 670 2 2
48 638 645 646 1 0
48 674 645 646 2 0
48 464 645 646 2 2
48 675 645 646 1 0
48 411 0 0 1 0
48 645 0 0 1 0
48 676 0 0 2 0
48 650 0 0 1 0
48 671 411 412 1 0
48 677 0 0 1 0
48 412 677 676 2 0
48 651 677 676 2 0
48 672 0 0 2 0
48 646 650 651 2 0
49 678 679 680 2 0
49 681 679 680 1 0
49 682 679 680 1 0
49 683 0 0 1 0
49 684 685 686 2 0
49 687 0 0 2 0
49 688 683 684 1 0
49 689 690 691 2 2
49 692 690 691 2 0
49 693 690 691 2 0
49 690 0 0 1 0
49 694 679 680 1 0
49 695 679 680 2 2
49 696 679 680 1 0
49 697 679 680 2 0
49 686 0 0 2 0
49 680 685 686 2 0
49 679 0 0 1 0
49 685 0 0 1 0
49 691 688 687 2 0
49 698 679 680 1 0
49 699 679 680 2 0
50 700 377 378 2 2
50 701 702 703 1 0
50 704 702 703 1 2
50 705 702 703 1 2
50 706 702 703 2 0
50 707 704 708 2 2
50 709 702 703 1 0
50 702 710 711 1 2
50 712 710 711 2 0
50 713 710 711 2 0
50 710 0 0 1 0
50 711 0 0 2 0
50 714 710 711 2 0
50 715 710 711 1 0
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62 913 0 0 2 2
62 912 0 0 1 0
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63 917 918 919 1 0
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63 916 920 921 2 2
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63 29 0 0 2 0
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63 449 0 0 2 0
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63 934 924 925 2 0
63 935 924 925 1 0
64 936 937 279 1 0
64 938 937 279 1 0
64 939 937 279 2 0
64 937 0 0 1 0
64 279 0 0 2 0
64 177 0 0 2 0
64 940 937 279 2 2
64 342 937 279 2 2
64 941 345 342 2 0
64 942 345 342 1 0
64 943 944 945 2 2
64 946 947 948 2 2
64 947 949 943 1 2
64 950 947 948 2 2
64 192 0 0 1 0
64 949 192 177 1 0
64 338 345 342 2 2
64 951 345 342 1 0
64 345 0 0 1 0
64 952 345 342 2 0
64 948 345 342 2 2
64 953 345 342 1 0
64 945 192 177 2 0
64 944 0 0 1 0
64 954 345 342 1 2
65 955 944 945 2 0
65 177 0 0 2 0
65 956 949 943 2 0
65 957 944 945 2 0
65 543 944 945 1 2
65 943 944 945 2 2
65 958 944 945 1 0
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65 947 949 943 1 2
65 192 0 0 1 0
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65 960 949 943 1 0
65 944 0 0 1 0
66 410 0 0 2 0
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66 333 427 410 2 2
66 962 427 410 2 0
66 427 0 0 1 0
66 963 427 410 2 0
This is only a small portion of my pedigree file. In this pedigree list there are about 400 repeated id; I want to replace repeated individual identifiers with new id and to replace them not only in id column but also in father and mother id columns. I don't want to remove subjects with the same id because they are useful for my heritability analysis. I use kinship package of R and it doesn't create a kinship matrix with repeated id.
Thank you for help
Best regards
Roberta
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