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Accessor and replacement functions for fpr slot

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

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

Usage

fpr(x, ...)

fpr(x, ...) <- value

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

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

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

Arguments

x

A COBRAPerformance or COBRAPlot object.

...

Additional arguments.

value

A data frame giving information about the observed FPR for each method and each stratification level, at various adjusted p-value thresholds.

Value

The accessor function returns a data frame giving information about the observed FPR for each method and each stratification level, at various adjusted p-value thresholds.

Author

Charlotte Soneson

Examples

data(cobradata_example)
cobraperf <- calculate_performance(cobradata_example,
                                   binary_truth = "status", aspects = "fpr")
#> Warning: Object doesn't have a slot sval. Please run update_cobradata(). For consistency, I will return an empty data.frame
#> column DESeq2 is being ignored for NBRS calculations
#> column DESeq2 is being ignored for FPR calculations
head(fpr(cobraperf))
#>       thr method basemethod   meas    fullmethod splitval NBR  TP  FP   TN  FN
#> 1 thr0.01  edgeR      edgeR __padj edgeR_overall  overall 686 499 187 1393 320
#> 2 thr0.01   voom       voom __padj  voom_overall  overall 684 502 182 1398 317
#> 3 thr0.05  edgeR      edgeR __padj edgeR_overall  overall 761 526 235 1345 293
#> 4 thr0.05   voom       voom __padj  voom_overall  overall 783 543 240 1340 276
#> 5  thr0.1  edgeR      edgeR __padj edgeR_overall  overall 836 552 284 1296 267
#> 6  thr0.1   voom       voom __padj  voom_overall  overall 866 568 298 1282 251
#>   TOT_CALLED DIFF NONDIFF        FPR
#> 1       2399  831    3027 0.06177734
#> 2       2399  831    3027 0.06012554
#> 3       2399  831    3027 0.07763462
#> 4       2399  831    3027 0.07928642
#> 5       2399  831    3027 0.09382227
#> 6       2399  831    3027 0.09844731