Mercurial > repos > stef > qdnaseq_test

comparison QDNAseq.R @ 7:1181e22c2b5a draft

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author stef
date Mon, 27 Oct 2014 05:24:59 -0400
parents d4d58887f008
children 238a698f7904
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6:d4d58887f008 7:1181e22c2b5a
142 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html' 142 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html'
143 PURE_CSS <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css' 143 PURE_CSS <- 'http://yui.yahooapis.com/pure/0.5.0/pure-min.css'
144 144
145 catMsg( "Starting QDNAseq wrapper" ) 145 catMsg( "Starting QDNAseq wrapper" )
146 catMsg( "Loading R libraries" ) 146 catMsg( "Loading R libraries" )
147 catMsg( R.version.string )
148
149 catMsg( "Loading Limma" )
150 library( "limma" )
151 catMsg( "Loading DNAcopy" )
152 library( "DNAcopy" )
153
154 ## supress msg to allow R to finish with non-error msg
147 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) ) 155 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) )
148 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) ) 156 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )
149 157
150 ## only one param: the tmp config file 158 ## only one param: the tmp config file
151 cmdLineArgs <- commandArgs(TRUE) 159 cmdLineArgs <- commandArgs(TRUE)