... | ... |
@@ -546,5 +546,5 @@ function (which expects ff objects and supports parallel processing) |
546 | 546 |
2010-08-25 M. Ritchie 1.7.12 |
547 | 547 |
** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina(). These make use of ff objects to store data. |
548 | 548 |
** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one. Also added a man page for this function |
549 |
-** Added a check for whether an object is an 'ff_matrix' before running open() or close() to several functions. Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize(). Added open() statement to stripNormalize(). |
|
549 |
+** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize(). Added open() statement to stripNormalize(). |
|
550 | 550 |
** tidied up crlmm-illumina.R, removing commented out code. |
... | ... |
@@ -142,11 +142,11 @@ readIdatFiles <- function(sampleSheet=NULL, |
142 | 142 |
protocolData(RG)[["ScanDate"]] = dates$scan |
143 | 143 |
} |
144 | 144 |
storageMode(RG) = "lockedEnvironment" |
145 |
- if(class(RG@assayData$R)[1]=="ff_matrix") { |
|
145 |
+# if(class(RG@assayData$R)[1]=="ff_matrix") { |
|
146 | 146 |
close(RG@assayData$R) |
147 | 147 |
close(RG@assayData$G) |
148 | 148 |
close(RG@assayData$zero) |
149 |
- } |
|
149 |
+# } |
|
150 | 150 |
RG |
151 | 151 |
} |
152 | 152 |
|
... | ... |
@@ -498,11 +498,11 @@ RGtoXY = function(RG, chipType, verbose=TRUE) { |
498 | 498 |
XY@assayData$zero[infI,] = 0 |
499 | 499 |
gc() |
500 | 500 |
|
501 |
- if(class(XY@assayData$X)[1]=="ff_matrix") { |
|
501 |
+# if(class(XY@assayData$X)[1]=="ff_matrix") { |
|
502 | 502 |
close(XY@assayData$X) |
503 | 503 |
close(XY@assayData$Y) |
504 | 504 |
close(XY@assayData$zero) |
505 |
- } |
|
505 |
+# } |
|
506 | 506 |
|
507 | 507 |
# storageMode(XY) = "lockedEnvironment" |
508 | 508 |
XY |
... | ... |
@@ -531,10 +531,10 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) { |
531 | 531 |
if (getRversion() > '2.7.0') pb <- txtProgressBar(min=0, max=max(stripnum), style=3) |
532 | 532 |
} |
533 | 533 |
|
534 |
- if(class(XY@assayData$X)[1]=="ff_matrix") { |
|
534 |
+# if(class(XY@assayData$X)[1]=="ff_matrix") { |
|
535 | 535 |
open(XY@assayData$X) |
536 | 536 |
open(XY@assayData$Y) |
537 |
- } |
|
537 |
+# } |
|
538 | 538 |
for(s in 1:max(stripnum)) { |
539 | 539 |
if(verbose) { |
540 | 540 |
if (getRversion() > '2.7.0') setTxtProgressBar(pb, s) |
... | ... |
@@ -554,10 +554,10 @@ stripNormalize = function(XY, useTarget=TRUE, verbose=TRUE) { |
554 | 554 |
rm(subX, subY, tmp, sel) |
555 | 555 |
gc() |
556 | 556 |
} |
557 |
- if(class(XY@assayData$X)[1]=="ff_matrix") { |
|
557 |
+# if(class(XY@assayData$X)[1]=="ff_matrix") { |
|
558 | 558 |
close(XY@assayData$X) |
559 | 559 |
close(XY@assayData$Y) |
560 |
- } |
|
560 |
+# } |
|
561 | 561 |
|
562 | 562 |
if(verbose) |
563 | 563 |
cat("\n") |
... | ... |
@@ -694,14 +694,14 @@ preprocessInfinium2 <- function(XY, mixtureSampleSize=10^5, |
694 | 694 |
t0 <- proc.time()-t0 |
695 | 695 |
if(verbose) message("Used ", round(t0[3],1), " seconds to save ", snpFile, ".") |
696 | 696 |
} |
697 |
- if(class(A)[1]=="ff_matrix") { |
|
697 |
+# if(class(A)[1]=="ff_matrix") { |
|
698 | 698 |
close(A) |
699 | 699 |
close(B) |
700 | 700 |
close(zero) |
701 | 701 |
close(SKW) |
702 | 702 |
close(mixtureParams) |
703 | 703 |
close(SNR) |
704 |
- } |
|
704 |
+# } |
|
705 | 705 |
return(res) |
706 | 706 |
} |
707 | 707 |
|