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Accessor and replacement functions for fsrnbrcurve slot

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

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

Usage

fsrnbrcurve(x, ...)

fsrnbrcurve(x, ...) <- value

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

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

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

Arguments

x

A COBRAPerformance or COBRAPlot object.

...

Additional arguments.

value

A data frame giving information necessary to generate curves of observed FSR vs number of features called positive for each method and each stratification level. If the object does not have an fsrnbrcurve 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 necessary to generate curves of observed FSR vs number of features called positive for each method and each stratification level.

Author

Charlotte Soneson

Examples

data(cobradata_example_sval)

cobraperf <- calculate_performance(cobradata_example_sval, 
                                   cont_truth = "logFC", 
                                   aspects = "fsrnbrcurve")
#> column Method3 is being ignored for FSRNBR calculations
head(fsrnbrcurve(cobraperf))
#>   FSR NBR       CUTOFF TS FS TOT_CALLED POSSIGN NEGSIGN ZEROSIGN  method
#> 1   0   1 3.154663e-47  1  0       2418     420     422     3016 Method1
#> 2   0   2 7.291524e-47  2  0       2418     420     422     3016 Method1
#> 3   0   3 1.186072e-46  3  0       2418     420     422     3016 Method1
#> 4   0   4 4.595996e-45  4  0       2418     420     422     3016 Method1
#> 5   0   6 1.075890e-44  6  0       2418     420     422     3016 Method1
#> 6   0   7 1.171043e-41  7  0       2418     420     422     3016 Method1
#>   basemethod   meas      fullmethod splitval
#> 1    Method1 __sval Method1_overall  overall
#> 2    Method1 __sval Method1_overall  overall
#> 3    Method1 __sval Method1_overall  overall
#> 4    Method1 __sval Method1_overall  overall
#> 5    Method1 __sval Method1_overall  overall
#> 6    Method1 __sval Method1_overall  overall