Mercurial > repos > stef > qdnaseq
changeset 31:2517af3f3475 draft
Uploaded
| author | stef |
|---|---|
| date | Wed, 18 Jun 2014 05:53:54 -0400 |
| parents | 647143d0c884 |
| children | 794a9cf2b2ed |
| files | QDNAseq.R |
| diffstat | 1 files changed, 11 insertions(+), 5 deletions(-) [+] |
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--- a/QDNAseq.R Wed Jun 18 05:45:02 2014 -0400 +++ b/QDNAseq.R Wed Jun 18 05:53:54 2014 -0400 @@ -177,8 +177,6 @@ DECIMALS <- 3 WEB_LINK <- 'http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html' - - catMsg( "Starting QDNAseq wrapper" ) catMsg( "Loading R libraries" ) suppressWarnings( suppressMessages( library( QDNAseq, quietly = TRUE ) ) ) @@ -186,7 +184,7 @@ systemUser <- system("whoami",T) qdnaseqVersion <- packageDescription( "QDNAseq" )$Version -catMsg( c(" Hello ", systemUser ) ) +catMsg( c("Analysis run with user: ", systemUser ) ) catMsg( c("QDNAseq version loaded: ", qdnaseqVersion) ) ## only one param: the tmp config file @@ -286,7 +284,7 @@ ## save objects to output dir saveRDS( readCounts, robjReadCoPath ); saveRDS( copyNumbersSmooth, robjCopyNrPath ); -exportBins(copyNumbersSmooth, file=igvCopyNrName, format="igv") +exportBins(copyNumbersSmooth, file=igvCopyNrPath, format="igv") ## also save objects for galaxy history output if requested if ( doOutputReadcountsRds ){ @@ -306,7 +304,7 @@ if ( doOutputCallsRds ){ saveRDS( copyNumbersCalled, calledSegmentsDatasetFile ); } - exportBins( copyNumbersCalled, file=igvCalledName, format="igv") + exportBins( copyNumbersCalled, file=igvCalledPath, format="igv") } @@ -375,6 +373,8 @@ copyNrSize <- paste( round( file.info( robjCopyNrPath )[["size"]] / 1000000, digits=2 ), 'MB' ) calledSize <- paste( round( file.info( robjCalledPath )[["size"]] / 1000000, digits=2 ), 'MB' ) regionSize <- paste( round( file.info( robjRegionPath )[["size"]] / 1000000, digits=2 ), 'MB' ) +igvCopyNrSize <- paste( round( file.info( igvCopyNrPath )[["size"]] / 1000000, digits=2 ), 'MB' ) +igvCalledSize <- paste( round( file.info( igvCallecPath )[["size"]] / 1000000, digits=2 ), 'MB' ) ## ------------------------ ## creating html output to be linked to from the middle galaxy pane @@ -440,6 +440,9 @@ cat( '<dd>QDNAseq object with copy numbers per bin, ', copyNrSize,'</dd>', "\n" ) r_code <- paste( r_code, '<code class="code">copyNumbersSmooth <- readRDS(', robjCopyNrName, ")</code><br />", sep="") + cat( '<dt>', htmlLink( path=igvCopyNrName, igvCopyNrName ), '</dt>', "\n" ) + cat( '<dd>IGV formatted text file with copy numbers per bin, ', igvCopyNrSize,'</dd>', "\n" ) + if ( doCall ){ cat( '<dt>', htmlLink( path=robjCalledName, robjCalledName ), '</dt>', "\n" ) cat( '<dd>QDNAseq object with segment and call status per bin, ', calledSize,'</dd>', "\n" ) @@ -449,6 +452,9 @@ cat( '<dd>list with segmented/called regions for each sample, ', regionSize, '</dd>', "\n" ) r_code <- paste( r_code, '<code class="code">calledRegions <- readRDS(', regiOutputName, ")</code><br />", sep="") + cat( '<dt>', htmlLink( path=igvCalledName, igvCalledName ), '</dt>', "\n" ) + cat( '<dd>IGV formatted text file with calls per bin , ', igvCalledSize,'</dd>', "\n" ) + } cat( '</dl></p>', "\n" )