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Accessor and replacement functions for fsrnbr slot

Source: R/AllGenerics.R, R/COBRAPerformance.R, R/COBRAPlot.R
fsrnbr.Rd

Accessor and replacement functions for the fsrnbr slot in a COBRAPerformance or COBRAPlot object.

Usage

fsrnbr(x, ...)

fsrnbr(x, ...) <- value

# S4 method for class 'COBRAPerformance'
fsrnbr(x)

# S4 method for class 'COBRAPerformance,data.frame'
fsrnbr(x) <- value

# S4 method for class 'COBRAPlot,data.frame'
fsrnbr(x) <- value

Arguments

x

A COBRAPerformance or COBRAPlot object.

...

Additional arguments.

value

A data frame giving information about the observed FSR and the number of features called positive for each method and each stratification level, at various s-value thresholds. If the object does not have an fsrnbr slot (older versions of the class did not have this slot), an empty data frame is returned for simplicity.

Value

The accessor function returns a data frame giving information about the observed FSR and the number of features called positive for each method and each stratification level, at various s-value thresholds.

Author

Charlotte Soneson

Examples

data(cobradata_example_sval)

cobraperf <- calculate_performance(cobradata_example_sval, 
                                   cont_truth = "logFC", 
                                   aspects = "fsrnbr")
#> column Method3 is being ignored for FSR/NBR calculations
head(fsrnbr(cobraperf))
#>       thr  method basemethod   meas      fullmethod splitval         FSR satis
#> 1 thr0.01 Method1    Method1 __sval Method1_overall  overall 0.000000000   yes
#> 2 thr0.01 Method2    Method2 __sval Method2_overall  overall 0.000000000   yes
#> 3 thr0.05 Method1    Method1 __sval Method1_overall  overall 0.001612903   yes
#> 4 thr0.05 Method2    Method2 __sval Method2_overall  overall 0.000000000   yes
#> 5  thr0.1 Method1    Method1 __sval Method1_overall  overall 0.002869440   yes
#> 6  thr0.1 Method2    Method2 __sval Method2_overall  overall 0.003072197   yes
#>         method.satis NBR  TS FS POSSIGN NEGSIGN ZEROSIGN TOT_CALLED
#> 1 Method1_overallyes 508 387  0     420     422     3016       2418
#> 2 Method2_overallyes 392 308  0     420     422     3016       2418
#> 3 Method1_overallyes 620 447  1     420     422     3016       2418
#> 4 Method2_overallyes 565 406  0     420     422     3016       2418
#> 5 Method1_overallyes 697 476  2     420     422     3016       2418
#> 6 Method2_overallyes 651 446  2     420     422     3016       2418