git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38364 bc3139a8-67e5-0310-9ffc-ced21a209358
unknown authored on 01/04/2009 06:24:30
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@@ -1,7 +1,7 @@ |
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Package: crlmm |
| 2 | 2 |
Type: Package |
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Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays. |
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-Version: 1.0.66 |
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+Version: 1.0.67 |
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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> |
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Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu> |
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@@ -1,7 +1,7 @@ |
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useDynLib("crlmm", .registration=TRUE)
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import(Biobase) |
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importFrom(affyio, read.celfile.header, read.celfile) |
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-importFrom(preprocessCore, normalize.quantiles.use.target) |
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+importFrom(preprocessCore, normalize.quantiles.use.target, normalize.quantiles) |
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| 5 | 5 |
importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar) |
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importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd) |
| 7 | 7 |
importFrom(genefilter, rowSds) |
| ... | ... |
@@ -50,8 +50,6 @@ crlmmIllumina(RG, XY, stripNorm=TRUE, useTarget=TRUE, |
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\item{badSNP}{'numeric'. Threshold to flag as bad SNP (affects batchQC)}
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} |
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\value{
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- \item{A}{normalized A allele intensity}
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- \item{B}{normalized B allele intensity}
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| 55 | 53 |
\item{calls}{Genotype calls (1 - AA, 2 - AB, 3 - BB)}
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| 56 | 54 |
\item{confs}{Confidence scores 'round(-1000*log2(1-p))'}
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| 57 | 55 |
\item{SNPQC}{SNP Quality Scores}
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