* collab_release:
remove trace() from vign.
only close callsGt when not missing
Fix the following bug in crlmmGT2 (only occurs when called from crlmm2):
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/crlmm@70636 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 18/10/2012 02:04:10
| ... | ... |
@@ -1,7 +1,7 @@ |
| 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: 1.16.0 |
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| 4 |
+Version: 1.16.1 |
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| 5 | 5 |
Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry |
| 6 | 6 |
Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| 7 | 7 |
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 |
| ... | ... |
@@ -208,7 +208,7 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL, |
| 208 | 208 |
callsGt.present <- !missing(callsGt) |
| 209 | 209 |
callsPr.present <- !missing(callsPr) |
| 210 | 210 |
overwriteAB <- !callsGt.present & !callsPr.present |
| 211 |
- if(overwriteAB){
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|
| 211 |
+ if(!overwriteAB){
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|
| 212 | 212 |
open(callsGt) |
| 213 | 213 |
open(callsPr) |
| 214 | 214 |
} |
| ... | ... |
@@ -246,7 +246,7 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL, |
| 246 | 246 |
close(A) |
| 247 | 247 |
close(B) |
| 248 | 248 |
close(mixtureParams) |
| 249 |
- if(overwriteAB){
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|
| 249 |
+ if(!overwriteAB){
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|
| 250 | 250 |
close(callsGt) |
| 251 | 251 |
close(callsPr) |
| 252 | 252 |
} |
| ... | ... |
@@ -22,7 +22,7 @@ |
| 22 | 22 |
options(width=60) |
| 23 | 23 |
options(continue=" ") |
| 24 | 24 |
options(prompt="R> ") |
| 25 |
-@ |
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| 25 |
+@ |
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| 26 | 26 |
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| 27 | 27 |
\section{Quick intro to \Rpackage{crlmm}}
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| 28 | 28 |
|
| ... | ... |
@@ -55,7 +55,7 @@ library(hapmapsnp6) |
| 55 | 55 |
path <- system.file("celFiles", package="hapmapsnp6")
|
| 56 | 56 |
celFiles <- list.celfiles(path, full.names=TRUE) |
| 57 | 57 |
system.time(crlmmResult <- crlmm(celFiles, verbose=FALSE)) |
| 58 |
-@ |
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| 58 |
+@ |
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| 59 | 59 |
|
| 60 | 60 |
The \Robject{crlmmResult} is a \Rclass{SnpSet} (see Biobase) object.
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| 61 | 61 |
\begin{itemize}
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| ... | ... |
@@ -72,7 +72,7 @@ The \Robject{crlmmResult} is a \Rclass{SnpSet} (see Biobase) object.
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| 72 | 72 |
calls(crlmmResult)[1:10,] |
| 73 | 73 |
confs(crlmmResult)[1:10,] |
| 74 | 74 |
crlmmResult[["SNR"]] |
| 75 |
-@ |
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| 75 |
+@ |
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| 76 | 76 |
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| 77 | 77 |
\section{Details}
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| 78 | 78 |
|
| ... | ... |
@@ -80,7 +80,7 @@ This document was written using: |
| 80 | 80 |
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| 81 | 81 |
<<>>= |
| 82 | 82 |
sessionInfo() |
| 83 |
-@ |
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| 83 |
+@ |
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| 84 | 84 |
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| 85 | 85 |
|
| 86 | 86 |
\end{document}
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