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modified man page for readGenCallOutput()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59249 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 14/10/2011 22:11:55
Showing 2 changed files

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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: 1.11.61
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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}