Convert object between COBRAPerformance and COBRAPlot classes.
Examples
data(cobradata_example)
cobraperf <- calculate_performance(cobradata_example,
binary_truth = "status",
aspects = "fdrtpr")
#> 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 TPR calculations
#> column DESeq2 is being ignored for FDR calculations
cobraplot <- prepare_data_for_plot(cobraperf)
## Coerce COBRAPerformance object into COBRAPlot object
as(cobraperf, "COBRAPlot")
#> An object of class "COBRAPlot"
#> @plotcolors
#> [1] ""
#>
#> @facetted
#> [1] TRUE
#>
#> @fdrtpr
#> 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 TPR FDR satis method.satis
#> 1 2399 831 3027 0.6004813 0.2725948 no edgeR_overallno
#> 2 2399 831 3027 0.6040915 0.2660819 no voom_overallno
#> 3 2399 831 3027 0.6329723 0.3088042 no edgeR_overallno
#> 4 2399 831 3027 0.6534296 0.3065134 no voom_overallno
#> 5 2399 831 3027 0.6642599 0.3397129 no edgeR_overallno
#> 6 2399 831 3027 0.6835138 0.3441109 no voom_overallno
#>
#> @fdrtprcurve
#> data frame with 0 columns and 0 rows
#>
#> @fdrnbr
#> data frame with 0 columns and 0 rows
#>
#> @fdrnbrcurve
#> data frame with 0 columns and 0 rows
#>
#> @fsrnbr
#> data frame with 0 columns and 0 rows
#>
#> @fsrnbrcurve
#> data frame with 0 columns and 0 rows
#>
#> @deviation
#> data frame with 0 columns and 0 rows
#>
#> @tpr
#> data frame with 0 columns and 0 rows
#>
#> @fpr
#> data frame with 0 columns and 0 rows
#>
#> @roc
#> data frame with 0 columns and 0 rows
#>
#> @scatter
#> data frame with 0 columns and 0 rows
#>
#> @fpc
#> data frame with 0 columns and 0 rows
#>
#> @overlap
#> data frame with 0 columns and 0 rows
#>
#> @corr
#> data frame with 0 columns and 0 rows
#>
#> @maxsplit
#> [1] 3
#>
#> @splv
#> [1] "none"
#>
#> @onlyshared
#> [1] FALSE
#>
## Coerce COBRAPlot object into COBRAPerformance object
as(cobraplot, "COBRAPerformance")
#> An object of class "COBRAPerformance"
#> @fdrtpr
#> 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 TPR FDR satis method.satis num_method
#> 1 2399 831 3027 0.6004813 0.2725948 no edgeR_overallno 1
#> 2 2399 831 3027 0.6040915 0.2660819 no voom_overallno 2
#> 3 2399 831 3027 0.6329723 0.3088042 no edgeR_overallno 1
#> 4 2399 831 3027 0.6534296 0.3065134 no voom_overallno 2
#> 5 2399 831 3027 0.6642599 0.3397129 no edgeR_overallno 1
#> 6 2399 831 3027 0.6835138 0.3441109 no voom_overallno 2
#>
#> @fdrtprcurve
#> data frame with 0 columns and 0 rows
#>
#> @fdrnbr
#> data frame with 0 columns and 0 rows
#>
#> @fdrnbrcurve
#> data frame with 0 columns and 0 rows
#>
#> @fsrnbr
#> data frame with 0 columns and 0 rows
#>
#> @fsrnbrcurve
#> data frame with 0 columns and 0 rows
#>
#> @deviation
#> data frame with 0 columns and 0 rows
#>
#> @tpr
#> data frame with 0 columns and 0 rows
#>
#> @fpr
#> data frame with 0 columns and 0 rows
#>
#> @roc
#> data frame with 0 columns and 0 rows
#>
#> @scatter
#> data frame with 0 columns and 0 rows
#>
#> @fpc
#> data frame with 0 columns and 0 rows
#>
#> @overlap
#> data frame with 0 columns and 0 rows
#>
#> @corr
#> data frame with 0 columns and 0 rows
#>
#> @maxsplit
#> [1] 3
#>
#> @splv
#> [1] "none"
#>
#> @onlyshared
#> [1] FALSE
#>