Report duplication stats on regions

getDupMatStats Report duplication stats based on the data calculated in the duplication matrix

getDupMatStats(DupMat)

Arguments

DupMat

The duplication matrix calculated by analyzeDuprates

Value

A data.frame containing the stats about the number of genes covered (1+ tags) and the number of genes containing duplicates (1+)

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
#> The following objects are masked from dupRadar_examples (pos = 8):
#> 
#>     dm, dm.bad
#> The following objects are masked from dupRadar_examples (pos = 9):
#> 
#>     dm, dm.bad

# call the plot and identify genes
getDupMatStats(DupMat=dm)
#>                   nRegions            nRegionsCovered 
#>               2.322800e+04               1.656900e+04 
#>            fRegionsCovered        nRegionsDuplication 
#>               7.133201e-01               2.015400e+04 
#>        fRegionsDuplication fCoveredRegionsDuplication 
#>               8.676597e-01               1.216368e+00