... | ... |
@@ -569,3 +569,7 @@ function (which expects ff objects and supports parallel processing) |
569 | 569 |
2010-10-07 M. Ritchie 1.7.20 |
570 | 570 |
** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf |
571 | 571 |
** tidied code and added snp.index to ffrowapply() in genotype.Illumina() when calls and confidence values are being updated in callSet. |
572 |
+ |
|
573 |
+2010-10-11 M. Ritchie 1.7.21 |
|
574 |
+** fixed bug with indexes for ffrowapply() in genotype.Illumina() |
|
575 |
+ |
... | ... |
@@ -1,8 +1,8 @@ |
1 | 1 |
Package: crlmm |
2 | 2 |
Type: Package |
3 | 3 |
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
4 |
-Version: 1.7.20 |
|
5 |
-Date: 2010-10-07 |
|
4 |
+Version: 1.7.21 |
|
5 |
+Date: 2010-10-11 |
|
6 | 6 |
Author: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry |
7 | 7 |
Maintainer: Benilton S Carvalho <carvalho@bclab.org>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
8 | 8 |
Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms |
... | ... |
@@ -1346,8 +1346,8 @@ processIDAT = function(sel, sampleSheet=NULL, |
1346 | 1346 |
open(res[["SNR"]]) |
1347 | 1347 |
open(res[["mixtureParams"]]) |
1348 | 1348 |
bb = ocProbesets()*length(sns)*8 |
1349 |
- ffrowapply(A[snp.index,][i1:i2, sel] <- res[["A"]][i1:i2, sel], X=res[["A"]], BATCHBYTES=bb) |
|
1350 |
- ffrowapply(B[snp.index,][i1:i2, sel] <- res[["B"]][i1:i2, sel], X=res[["B"]], BATCHBYTES=bb) |
|
1349 |
+ ffrowapply(A[snp.index,][i1:i2, sel] <- res[["A"]][i1:i2, ], X=res[["A"]], BATCHBYTES=bb) |
|
1350 |
+ ffrowapply(B[snp.index,][i1:i2, sel] <- res[["B"]][i1:i2, ], X=res[["B"]], BATCHBYTES=bb) |
|
1351 | 1351 |
if(length(np.index)>0) { |
1352 | 1352 |
for (j in sel) { |
1353 | 1353 |
A[np.index, j] = res[["cnAB"]]$A[,j] |