Mercurial > repos > stef > qdnaseq
comparison QDNAseq.R @ 25:8509c112abaa draft
Uploaded
| author | stef |
|---|---|
| date | Wed, 18 Jun 2014 05:05:19 -0400 |
| parents | 336697c6f7fa |
| children | 2efda0ed7ccf |
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| 24:9f4e0192de10 | 25:8509c112abaa |
|---|---|
| 181 | 181 |
| 182 catMsg( "Starting QDNAseq wrapper" ) | 182 catMsg( "Starting QDNAseq wrapper" ) |
| 183 catMsg( "Loading R libraries" ) | 183 catMsg( "Loading R libraries" ) |
| 184 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) ) | 184 suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) ) |
| 185 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) ) | 185 suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) ) |
| 186 suppressWarnings( suppressMessages( library( matrixStats, quietly = TRUE ) ) ) | 186 |
| 187 qdnaseqVersion <- packageDescription( "QDNAseq" )$Version | |
| 188 qdnaseqDate <- packageDescription( "QDNAseq" )$Date | |
| 189 catMsg( "QDNAseq info: version(", qdnaseqVersion, ") and date (", qdnaseqDate, ")" ) | |
| 187 | 190 |
| 188 ## only one param: the tmp config file | 191 ## only one param: the tmp config file |
| 189 cmdLineArgs <- commandArgs(TRUE) | 192 cmdLineArgs <- commandArgs(TRUE) |
| 190 config <- cmdLineArgs[1] | 193 config <- cmdLineArgs[1] |
| 191 | 194 |
| 452 r_code <- paste( r_code, '<code class="code">calledRegions <- readRDS(', regiOutputName, ")</code><br />", sep="") | 455 r_code <- paste( r_code, '<code class="code">calledRegions <- readRDS(', regiOutputName, ")</code><br />", sep="") |
| 453 | 456 |
| 454 } | 457 } |
| 455 cat( '</dl></p>', "\n" ) | 458 cat( '</dl></p>', "\n" ) |
| 456 | 459 |
| 457 cat( r_code, "</p>\n", sep="\n") | 460 #cat( r_code, "</p>\n", sep="\n") |
| 458 cat( '<p>See ', htmlLink( WEB_LINK, 'the bioconductor QDNAseq documentation' ), ' for more information on how to work with these files</p>', "\n", sep='' ) | 461 cat( '<p>See ', htmlLink( WEB_LINK, 'the bioconductor QDNAseq documentation' ), ' for more information on how to work with these files</p>', "\n", sep='' ) |
| 459 | 462 |
| 460 ## ------------------------ | 463 ## ------------------------ |
| 461 ## table with links to files | 464 ## table with links to files |
| 462 ## ------------------------ | 465 ## ------------------------ |