git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59249 bc3139a8-67e5-0310-9ffc-ced21a209358
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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: 1.11.61 |
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+Version: 1.11.62 |
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Date: 2010-12-10 |
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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 |
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Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
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@@ -19,10 +19,9 @@ readGenCallOutput(file, path=".", cdfName, colnames=list("SampleID"="Sample ID", |
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('human370v1c', human550v3b', 'human650v3a', 'human1mv1c', |
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'human370quadv3c', 'human610quadv1b', 'human660quadv1a', |
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'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'humancytosnp12v2p1h')} |
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- \item{cdfName}{'character' defining the chip annotation (manifest) to use |
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\item{colnames}{list containing elements 'SampleID', 'SNPID', 'XRaw' and 'YRaw', which specify the column names from |
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- in 'file' that pertain to these variables. The default should suffice in most situations. |
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- \item{type}{list containing data types for the columns to be read in. The default should be fine in most situations. |
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+ in 'file' that pertain to these variables. The default should suffice in most situations.} |
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+ \item{type}{list containing data types for the columns to be read in. The default should be fine in most situations.} |
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\item{verbose}{'logical'. Should processing information be displayed as data is read in?} |
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} |
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@@ -45,10 +44,8 @@ The function crlmmillumina() can be run on the output of the \code{readGenCallOu |
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\author{Cynthia Liu and Matt Ritchie} |
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\examples{ |
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- |
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#XY = readGenCallOutput(file="Hap650Yv3_Final_Report.txt", cdfName="human650v3a") |
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#crlmmOut = crlmmIllumina(XY=XY) |
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- |
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} |
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\keyword{IO} |