git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@39171 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 27/04/2009 14:11:59
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@@ -147,3 +147,7 @@ is decoded and scanned |
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2009-04-09 R Scharpf - committed version 1.0.81 |
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* added a skeleton of a copy number vignette for the illumina platform (illumina_copynumber.Rnw) to inst/scripts |
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+ |
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+2009-04-27 R Scharpf - committed version 1.3.1 |
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+* Fixed bug in nonpolymorphic() function |
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@@ -1,7 +1,7 @@ |
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Package: crlmm |
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Type: Package |
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Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
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-Version: 1.3.0 |
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+Version: 1.3.1 |
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Date: 2008-12-30 |
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Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
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Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
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@@ -440,7 +440,11 @@ nonpolymorphic <- function(plateIndex, NP, envir, CONF.THR=0.99, DF.PRIOR=50, pk |
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muB <- muB[!flagsB, "BB"] |
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X <- cbind(1, log2(c(muA, muB))) |
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Y <- log2(c(phiA[!flagsA], phiB[!flagsB])) |
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- if(nrow(X) > 5000) ix <- sample(1:nrow(X), 5000) |
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+ if(nrow(X) > 5000){
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+ ix <- sample(1:nrow(X), 5000) |
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+ } else {
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+ ix <- 1:nrow(X) |
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+ } |
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##X <- X[ix, ] |
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##Y <- Y[ix] |
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betahat <- solve(crossprod(X[ix, ]), crossprod(X[ix, ], Y[ix])) |