comparison QDNAseq.R @ 30:647143d0c884 draft

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29:4c4e4d88779c

	## have to set R output options otherwise scientific method is used at some point
	options( "scipen"=100 )

	sampleCount <- length( regionsList )
	sampleNames <- names( regionsList )
	systemUser <- system("whoami",T)
	bedgraphColumns <- c( 'chr', 'start', 'end', 'segmentval' )

	cat( MAIN_NAME, " Hello ", systemUser, "!!\n", sep="")
	cat( MAIN_NAME, " There are ", sampleCount, " samples found in input list...\n", sep="")

	for ( sample in sampleNames ){		
		cat( MAIN_NAME, " Working on sample ", sample, "\n", sep="")
		regionCount <- nrow( regionsList[[sample]] )

MAIN_NAME <- '[INFO] '
CSS_FILE  <- paste( TOOL_PATH, '/QDNAseq.css', sep="" )
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 ) ) )
suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )

qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
qdnaseqDate <- packageDescription( "QDNAseq" )$Date
catMsg( paste("QDNAseq info: version(", qdnaseqVersion, ") and date (", qdnaseqDate, ")", sep="") )

## only one param: the tmp config file
cmdLineArgs <- commandArgs(TRUE)
config      <- cmdLineArgs[1]

		region_count <- nrow( data.frame( regions[[ sample ]] ) )
		cat( MAIN_NAME, ' sample "', sample, '" has ', region_count, " regions\n", sep="" )
		plotted_images[[ sample ]][[ 'region_count' ]] <- region_count
	}

	## add read counts
	catMsg( "Used")
	catMsg( usedReads )

	plotted_images[[ sample ]][[ 'usedReads'  ]] <- usedReads
}
#cat( MAIN_NAME, "PLOTTED_IMAGES: ", names(plotted_images), "\n", sep="" )

if ( doCall ){
	saveRDS( regions, robjRegionPath )
	printedFiles <- outputRegionsFromList( regions, outputBasename=outputName, outputDir=outputPath )	
}

30:647143d0c884

	## have to set R output options otherwise scientific method is used at some point
	options( "scipen"=100 )

	sampleCount <- length( regionsList )
	sampleNames <- names( regionsList )
	bedgraphColumns <- c( 'chr', 'start', 'end', 'segmentval' )
	
	cat( MAIN_NAME, " There are ", sampleCount, " samples found in input list...\n", sep="")

	for ( sample in sampleNames ){		
		cat( MAIN_NAME, " Working on sample ", sample, "\n", sep="")
		regionCount <- nrow( regionsList[[sample]] )

MAIN_NAME <- '[INFO] '
CSS_FILE  <- paste( TOOL_PATH, '/QDNAseq.css', sep="" )
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 ) ) )
suppressWarnings( suppressMessages( library( CGHcall, quietly = TRUE ) ) )

systemUser <- system("whoami",T)
qdnaseqVersion <- packageDescription( "QDNAseq" )$Version
catMsg( c(" Hello ", systemUser ) )
catMsg( c("QDNAseq version loaded: ", qdnaseqVersion) )

## only one param: the tmp config file
cmdLineArgs <- commandArgs(TRUE)
config      <- cmdLineArgs[1]

		region_count <- nrow( data.frame( regions[[ sample ]] ) )
		cat( MAIN_NAME, ' sample "', sample, '" has ', region_count, " regions\n", sep="" )
		plotted_images[[ sample ]][[ 'region_count' ]] <- region_count
	}

	## add USED read counts
	plotted_images[[ sample ]][[ 'usedReads'  ]] <- usedReads
}

if ( doCall ){
	saveRDS( regions, robjRegionPath )
	printedFiles <- outputRegionsFromList( regions, outputBasename=outputName, outputDir=outputPath )	
}