git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@52806 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 16/02/2011 15:56:27 | ... | ... |
@@ -474,7 +474,6 @@ ACN <- function(object, allele, i , j){
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| 474 | 474 |
jj <- which(object$gender[j] == 2) |
| 475 | 475 |
acn[acn.index, jj] <- C1(object, marker.index, female.batch.index, female.index) |
| 476 | 476 |
} |
| 477 |
-## ## 4. CHR X NPs: men |
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| 478 | 477 |
male.index <- j[object$gender[j] == 1] |
| 479 | 478 |
if(length(male.index) > 0){
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| 480 | 479 |
if(is.ff){
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| ... | ... |
@@ -508,32 +507,27 @@ ACN <- function(object, allele, i , j){
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| 508 | 507 |
acn[acn.index, ] <- 0 |
| 509 | 508 |
} |
| 510 | 509 |
if(any(is.auto)){
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| 511 |
- auto.index <- which(is.auto & is.snp) |
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| 512 |
- if(length(auto.index) > 0){
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- marker.index <- i[auto.index] |
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- acn[auto.index, ] <- C2(object, marker.index, batch.index, j) |
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| 515 |
- } |
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| 510 |
+ auto.index <- which(is.auto) |
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| 511 |
+ marker.index <- i[is.auto] |
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| 512 |
+ acn[auto.index, ] <- C2(object, marker.index, batch.index, j) |
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| 516 | 513 |
} |
| 517 | 514 |
if(any(is.X)){
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| 518 |
- ##Chr X SNPs |
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| 519 |
- if(any(is.snp)){
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- if(is.ff) {
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- open(phiPrimeA(object)) |
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| 522 |
- open(phiPrimeB(object)) |
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| 523 |
- open(phiA(object)) |
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| 524 |
- open(nuA(object)) |
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| 525 |
- open(A(object)) |
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- } |
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| 527 |
- marker.index <- i[is.X & is.snp] |
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- acn.index <- which(is.X & is.snp) |
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- acn[acn.index, ] <- C3(object, allele="B", marker.index, batch.index, j) |
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| 530 |
- if(is.ff) {
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- close(phiPrimeA(object)) |
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| 532 |
- close(phiPrimeB(object)) |
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- close(phiA(object)) |
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| 534 |
- close(nuA(object)) |
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| 535 |
- close(A(object)) |
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| 536 |
- } |
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| 515 |
+ if(is.ff){
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| 516 |
+ open(phiPrimeA(object)) |
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| 517 |
+ open(phiPrimeB(object)) |
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| 518 |
+ open(phiA(object)) |
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| 519 |
+ open(nuA(object)) |
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+ open(A(object)) |
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| 521 |
+ } |
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+ marker.index <- i[is.X & is.snp] |
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| 523 |
+ acn.index <- which(is.X & is.snp) |
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| 524 |
+ acn[acn.index, ] <- C3(object, allele="B", marker.index, batch.index, j) |
|
| 525 |
+ if(is.ff){
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|
| 526 |
+ close(phiPrimeA(object)) |
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| 527 |
+ close(phiPrimeB(object)) |
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| 528 |
+ close(phiA(object)) |
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| 529 |
+ close(nuA(object)) |
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| 530 |
+ close(A(object)) |
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| 537 | 531 |
} |
| 538 | 532 |
if(any(!is.snp)){
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| 539 | 533 |
acn.index <- which(!is.snp) |