git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@101808 bc3139a8-67e5-0310-9ffc-ced21a209358
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@@ -2,8 +2,8 @@ Package: crlmm |
2 | 2 |
Type: Package |
3 | 3 |
Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for |
4 | 4 |
Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
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-Version: 1.25.0 |
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-Date: Thu Sep 25 21:06:19 EST 2014 |
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+Version: 1.25.1 |
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+Date: Sat Oct 18 14:34:17 EST 2014 |
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7 | 7 |
Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo |
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Ruczinski, Rafael A Irizarry |
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Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, |
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@@ -1260,7 +1260,8 @@ genotype.Illumina <- function(sampleSheet=NULL, |
1260 | 1260 |
"humanomni258v1a", # Omni2.5 8 v1 A |
1261 | 1261 |
"humanomni258v1p1b", # Omni2.5 8 v1.1 B |
1262 | 1262 |
"humanomni5quadv1b", # Omni5 quad |
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- "humanexome12v1p2a") # Exome 12 v1.2 A |
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+ "humanexome12v1p2a", # Exome 12 v1.2 A |
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+ "humanomniexpexome8v1p1b") # Omni Express Exome 8 v1.1b |
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crlmm.supported = c("human1mv1c", # 1M |
1265 | 1266 |
"human370v1c", # 370CNV |
1266 | 1267 |
"human650v3a", # 650Y |
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@@ -159,10 +159,10 @@ calculatePriorValues <- function(M, numSNP, verbose) { |
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stopCluster(cl) |
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centers <- matrix(centers, numSNP, 3, byrow = TRUE) |
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priormeans = apply(centers, 2, FUN="median", na.rm=TRUE) |
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- if(abs(sum(priormeans))>1) |
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- checksymmetric= apply(centers,1,function(x){abs(sum(x))})<1 |
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+ if(abs(sum(priormeans))>1) { |
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+ checksymmetric= apply(centers,1,function(x){abs(sum(x))})<1 |
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priormeans=apply(centers[checksymmetric,],2, FUN="median", na.rm=TRUE) |
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- |
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+ } |
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if (verbose) message("Done calculating Prior Means") |
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return(priormeans) |
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} |