git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58639 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 01/10/2011 04:47:47 | ... | ... |
@@ -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: 1.11.18 |
|
| 4 |
+Version: 1.11.19 |
|
| 5 | 5 |
Date: 2010-12-10 |
| 6 | 6 |
Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, 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 <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| ... | ... |
@@ -433,6 +433,7 @@ setMethod("xyplotcrlmm", signature(x="formula", data="CNSet", predictRegion="lis
|
| 433 | 433 |
gt.conf=as.numeric(confs(data)), |
| 434 | 434 |
snpid=fns)#, snp=snpId) |
| 435 | 435 |
df <- as.data.frame(df) |
| 436 |
+ df$snpid <- factor(df$snpid, levels=unique(df$snpid), ordered=TRUE) |
|
| 436 | 437 |
bns <- batchNames(data) |
| 437 | 438 |
predictRegion <- lapply(predictRegion, function(x, bns){
|
| 438 | 439 |
batch.index <- match(bns, dimnames(x$mu)[[3]]) |
| ... | ... |
@@ -440,7 +441,6 @@ setMethod("xyplotcrlmm", signature(x="formula", data="CNSet", predictRegion="lis
|
| 440 | 441 |
x$cov <- x$cov[, , batch.index, drop=FALSE] |
| 441 | 442 |
return(x) |
| 442 | 443 |
}, bns=bns) |
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- df$snpid <- as.character(df$snpid) |
|
| 444 | 444 |
##df <- as.data.frame(data) |
| 445 | 445 |
xyplot(x, df, predictRegion=predictRegion, ...) |
| 446 | 446 |
}) |