Duplication rate ~ total read count plot

duprateExpPlot Duplication rate ~ total read count plot

duprateExpPlot(
  DupMat,
  tNoAlternative = TRUE,
  tRPKM = TRUE,
  tRPKMval = 0.5,
  addLegend = TRUE,
  ...
)

Arguments

DupMat

The duplication matrix calculated by analyzeDuprates

tNoAlternative

Display threshold of 1000 reads per kilobase

tRPKM

Display threshold at a given RPKM level

tRPKMval

The given RPKM level

addLegend

Whether to add a legend to the plot

...

Other parameters sent to smoothScatter()

Value

nothing

Details

This function makes a smooth scatter plot showing the per gene duplication rate versus the total read count.

Examples

# dm is a duplication matrix calculated by analyzeDuprates:
# R> dm <- analyzeDuprates(bamDuprm,gtf,stranded,paired,threads)
attach(dupRadar_examples)
#> The following objects are masked from dupRadar_examples (pos = 3):
#> 
#>     dm, dm.bad
#> The following objects are masked from dupRadar_examples (pos = 4):
#> 
#>     dm, dm.bad
#> The following objects are masked from dupRadar_examples (pos = 5):
#> 
#>     dm, dm.bad
#> The following objects are masked from dupRadar_examples (pos = 6):
#> 
#>     dm, dm.bad
#> The following objects are masked from dupRadar_examples (pos = 7):
#> 
#>     dm, dm.bad

# duprate plot
duprateExpPlot(DupMat=dm)