Dear R experts,
I have 3 matrices - "Mx", "My" and "geno" that have the same exact dimensions
(attached). I want to calculate a expression matrix (ME) of the same dimension
as well. It is a little complicated.
To calculate and for a specific cell in ME, e.g. ME[2,2],
if value of geno[2,2] is 0, ME[2,2]=Mx[2,2]+My[2,2];
if value of geno[2,2] is 1, ME[2,2]=the larger number of Mx[2,2] and My[2,2]
if value of geno[2,2] is NA, ME[2,2]=NA
I tried to make codes below, but did not work and got stuck. I was wondering if
anyone could help with better coding.
Thanks in advance,
Zhengyu
-----------------------------------------------
Mx <- read.table("Mx.txt",header=TRUE, sep="\t", na.strings="NA", dec=".",
strip.white=TRUE)
My <- read.table("My.txt",header=TRUE, sep="\t", na.strings="NA", dec=".",
strip.white=TRUE)
geno <- read.table("geno.txt",header=TRUE, sep="\t", na.strings="NA", dec=".",
strip.white=TRUE)
#Calculate Exp for geno==0
ind=which(geno==0,arr.ind=T)
het=Mx+My
ME=matrix(het,nrow=nrow(geno),ncol=ncol(geno))
ME[ind]=het[ind]
#Calculate Exp for geno==1
ind=which(geno==1,arr.ind=T)
hom=apply(M1,c(1:2),function(x)max(M1[],M2[]))# error
ME=matrix(hom,nrow=nrow(geno),ncol=ncol(geno))
ME[ind]=hom[ind]
# I think the first calculation (geno==0) will be replaced but I don't know how
to keep them.
> head(Mx)
X1cX X2cX X3cX X4cX X5cX X6cX X7cX X8cX
1 26383 6252 14319 16421 2225 480 2038 1164
2 636 310 351 341 218 656 412 267
3 301 299 752 236 239 309 283 195
4 1016 1046 1364 782 822 274 437 346
5 1261 1272 1076 1037 659 337 1143 1195
6 609 414 393 459 215 429 566 236
> dim(Mx)
[1] 20 8
> head(My)
X1cY X2cY X3cY X4cY X5cY X6cY X7cY X8cY
1 1039 233 408 607 275 1837 1319 149
2 7146 1706 2248 2346 1596 544 2696 417
3 266 425 1186 214 325 369 377 215
4 260 282 238 240 264 265 317 203
5 1070 1052 746 613 384 447 456 683
6 13032 1708 2328 5998 2529 923 1068 145
> dim(My)
[1] 20 8
> head(geno)
P1 P2 P3 P4 P5 P6 P7 P8
1 NA NA NA NA 1 NA NA NA
2 1 1 1 1 1 1 1 1
3 1 1 0 0 0 0 1 0
4 1 1 1 1 1 1 0 0
5 0 0 0 0 0 0 1 0
6 NA NA NA NA NA NA NA NA
> dim(geno)
[1] 20 8
X1cX X2cX X3cX X4cX X5cX X6cX X7cX X8cX
26383 6252 14319 16421 2225 480 2038 1164
636 310 351 341 218 656 412 267
301 299 752 236 239 309 283 195
1016 1046 1364 782 822 274 437 346
1261 1272 1076 1037 659 337 1143 1195
609 414 393 459 215 429 566 236
1150 394 478 662 430 430 511 168
503 414 328 340 348 609 242 235
701 1629 569 447 472 247 705 646
1478 923 1447 1623 1243 830 1212 2819
2511 914 1553 1834 497 567 537 528
1551 622 789 361 245 192 269 480
406 543 503 370 322 421 205 265
442 553 538 295 162 391 220 258
543 106 344 332 442 286 235 205
394 317 223 192 99 290 251 269
433 492 672 278 373 329 562 709
354 292 424 382 218 333 254 279
1863 1823 1176 785 552 332 471 212
496 285 307 363 170 471 381 623
X1cY X2cY X3cY X4cY X5cY X6cY X7cY X8cY
1039 233 408 607 275 1837 1319 149
7146 1706 2248 2346 1596 544 2696 417
266 425 1186 214 325 369 377 215
260 282 238 240 264 265 317 203
1070 1052 746 613 384 447 456 683
13032 1708 2328 5998 2529 923 1068 145
18068 8188 7103 13441 8262 4016 5952 259
221 201 175 178 156 142 234 133
399 643 389 1953 225 638 483 396
1578 2284 1283 1724 1476 1458 1186 508
488 506 460 679 509 288 489 407
538 340 694 594 137 281 223 230
852 314 266 181 169 152 226 249
291 180 219 89 120 167 110 152
168 212 125 203 313 339 280 239
256 111 203 138 117 163 174 145
9721 11517 11662 11110 9392 4029 11070 14861
216 180 183 163 102 153 164 136
216 160 181 271 115 128 154 87
108 148 200 156 154 113 243 239
P1 P2 P3 P4 P5 P6 P7 P8
NA NA NA NA 1 NA NA NA
1 1 1 1 1 1 1 1
1 1 0 0 0 0 1 0
1 1 1 1 1 1 0 0
0 0 0 0 0 0 1 0
NA NA NA NA NA NA NA NA
1 1 1 1 1 1 1 1
0 0 0 1 0 0 1 0
1 1 1 1 1 1 1 1
NA 1 NA NA NA NA NA 1
1 1 1 1 1 1 1 1
1 0 0 1 0 1 1 1
1 0 0 1 0 1 1 0
NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA
1 1 0 1 0 1 0 0
NA NA NA NA NA NA NA NA
NA NA NA NA NA NA NA NA
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