Accessor and replacement functions for overlap slot

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

Usage

overlap(x, ...)

overlap(x, ...) <- value

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

# S4 method for class 'COBRAPerformance,list_df'
overlap(x) <- value

# S4 method for class 'COBRAPlot,list_df'
overlap(x) <- value

Arguments

x

A COBRAPerformance or COBRAPlot object.

...

Additional arguments.

value

A data frame or a list, giving information about which feature that are classified as 'positive' by each method and for each stratification level.

Value

The accessor function returns a data frame or a list, giving information about which feature that are classified as 'positive' by each method and for each stratification level.

Author

Charlotte Soneson

Examples

data(cobradata_example)
cobraperf <- calculate_performance(cobradata_example,
                                   binary_truth = "status",
                                   aspects = "overlap")
#> Warning: Object doesn't have a slot sval. Please run update_cobradata(). For consistency, I will return an empty data.frame
head(overlap(cobraperf))
#>                 edgeR voom truth
#> ENSG00000000457     0    0     0
#> ENSG00000000460     0    0     0
#> ENSG00000000938     0    0     0
#> ENSG00000000971     0    0     0
#> ENSG00000001460     1    1     1
#> ENSG00000001461     0    0     1