@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.11.61

+Version: 1.11.62

 Date: 2010-12-10

 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

 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -19,10 +19,9 @@ readGenCallOutput(file, path=".", cdfName, colnames=list("SampleID"="Sample ID",

     ('human370v1c', human550v3b', 'human650v3a', 'human1mv1c',

     'human370quadv3c', 'human610quadv1b', 'human660quadv1a',

     'human1mduov3b', 'humanomni1quadv1b', 'humanomniexpress12v1b', 'humancytosnp12v2p1h')}

-  \item{cdfName}{'character' defining the chip annotation (manifest) to use

   \item{colnames}{list containing elements 'SampleID', 'SNPID', 'XRaw' and 'YRaw', which specify the column names from

-     in 'file' that pertain to these variables.  The default should suffice in most situations. 

-  \item{type}{list containing data types for the columns to be read in.  The default should be fine in most situations.

+     in 'file' that pertain to these variables.  The default should suffice in most situations.}

+  \item{type}{list containing data types for the columns to be read in.  The default should be fine in most situations.}

   \item{verbose}{'logical'.  Should processing information be displayed as data is read in?}

 }

@@ -45,10 +44,8 @@ The function crlmmillumina() can be run on the output of the \code{readGenCallOu

 \author{Cynthia Liu and Matt Ritchie}

 \examples{

-

 #XY = readGenCallOutput(file="Hap650Yv3_Final_Report.txt", cdfName="human650v3a")

 #crlmmOut = crlmmIllumina(XY=XY)

-

 }

 \keyword{IO}