Nothing
# In R:
library(PACVr)
gbkFile <- system.file("extdata", "NC_045072/NC_045072.gb", package="PACVr")
bamFile <- system.file("extdata", "NC_045072/NC_045072_subsampled.bam",
package="PACVr")
outFile <- paste(tempdir(), "/NC_045072_CoverageViz.pdf", sep="")
#outFile <- "../NC_045072_CoverageViz.pdf" # on R-Studio for Windows
#outFile <- "~/NC_045072_CoverageViz.pdf" # on R-Studio for Linux
exitStatusVec <- c() # useful for large automated jobs
## ONLY COVERAGE VALUES, NO REGION INDICATORS ##
exitStatus <- PACVr.complete(gbkFile, bamFile, windowSize=250, logScale=FALSE,
threshold=0.5, relative=TRUE, textSize=0.5,
output=outFile)
exitStatusVec <- c(exitStatusVec, exitStatus)
## COVERAGE VALUES PLUS REGION INDICATORS ##
exitStatus <- PACVr.complete(gbkFile, bamFile, windowSize=250, logScale=FALSE,
threshold=0.5, relative=TRUE, textSize=0.5,
IRCheck=0, output=outFile)
exitStatusVec <- c(exitStatusVec, exitStatus)
## COVERAGE VALUES PLUS REGION INDICATORS PLUS IR SYNTENY LINES ##
exitStatus <- PACVr.complete(gbkFile, bamFile, windowSize=250, logScale=FALSE,
threshold=0.5, relative=TRUE, textSize=0.5,
IRCheck=1, output=outFile)
exitStatusVec <- c(exitStatusVec, exitStatus)
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