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Subsetting COBRAData, COBRAPerformance or COBRAPlot objects

Source: R/COBRAData.R, R/COBRAPerformance.R, R/COBRAPlot.R
Extract.Rd

Functions to subset COBRAData, COBRAPerformance or COBRAPlot objects. COBRAData objects are subset by features (rows), while COBRAPerformance and COBRAPlot objects are subset by methods (columns). Numeric indices are not allowed, since not all slots may be arranged in the same order.

Usage

# S4 method for class 'COBRAData'
x[i, j = "missing", drop = "missing"]

# S4 method for class 'COBRAPerformance'
x[i = "missing", j, drop = "missing"]

# S4 method for class 'COBRAPlot'
x[i = "missing", j, drop = "missing"]

Arguments

x

A COBRAData, COBRAPerformance or COBRAPlot object.

i

For COBRAData objects, a character vector of feature names to retain.

j

For COBRAPerformance and COBRAPlot objects, a character vector with method names to retain.

drop

not used.

Value

A subset of the original object, of the same class

Examples

data(cobradata_example)
cobradata_example[c("ENSG00000000457", "ENSG00000000971",
                    "ENSG00000000460"), ]
#> An object of class "COBRAData"
#> @pval
#>                     edgeR       voom     DESeq2
#> ENSG00000000457 0.1178024 0.05147484 0.01627063
#> ENSG00000000971 0.8449686 0.89394930 0.96278259
#> ENSG00000000460 0.1101413 0.12767845 0.03281416
#> 
#> @padj
#>                     edgeR      voom
#> ENSG00000000457 0.2833295 0.1375146
#> ENSG00000000971 0.9382227 0.9492325
#> ENSG00000000460 0.2700376 0.2826398
#> 
#> @sval
#> data frame with 0 columns and 3 rows
#> 
#> @score
#>                      edgeR       voom      DESeq2
#> ENSG00000000457 0.22706080 0.23980596 0.274811698
#> ENSG00000000971 0.03900847 0.02263371 0.008182751
#> ENSG00000000460 0.31050478 0.27677537 0.359226203
#> 
#> @truth
#>                 status n_isoforms logFC       logFC_cat       expr
#> ENSG00000000457      0          5     0 [ 0.000, 0.297)   8.525774
#> ENSG00000000971      0          6     0 [ 0.000, 0.297) 163.547797
#> ENSG00000000460      0         10     0 [ 0.000, 0.297)   3.314544
#>                            expr_cat
#> ENSG00000000457 [2.85e+00,1.45e+01)
#> ENSG00000000971 [1.45e+01,2.43e+04]
#> ENSG00000000460 [2.85e+00,1.45e+01)
#> 
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
cobraperf[, c("voom")]
#> An object of class "COBRAPerformance"
#> @fdrtpr
#>       thr method basemethod   meas   fullmethod splitval NBR  TP  FP   TN  FN
#> 2 thr0.01   voom       voom __padj voom_overall  overall 684 502 182 1398 317
#> 4 thr0.05   voom       voom __padj voom_overall  overall 783 543 240 1340 276
#> 6  thr0.1   voom       voom __padj voom_overall  overall 866 568 298 1282 251
#>   TOT_CALLED DIFF NONDIFF       TPR       FDR satis   method.satis
#> 2       2399  831    3027 0.6040915 0.2660819    no voom_overallno
#> 4       2399  831    3027 0.6534296 0.3065134    no voom_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
#> 
cobraplot <- prepare_data_for_plot(cobraperf)
cobraplot[, c("voom")]
#> Object up to date
#> An object of class "COBRAPlot"
#> @plotcolors
#>            voom    voom_overall         voomyes voom_overallyes          voomno 
#>       "#00BFC4"       "#00BFC4"       "#00BFC4"       "#00BFC4"         "white" 
#>  voom_overallno 
#>         "white" 
#> 
#> @facetted
#> [1] TRUE
#> 
#> @fdrtpr
#>       thr method basemethod   meas   fullmethod splitval NBR  TP  FP   TN  FN
#> 2 thr0.01   voom       voom __padj voom_overall  overall 684 502 182 1398 317
#> 4 thr0.05   voom       voom __padj voom_overall  overall 783 543 240 1340 276
#> 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
#> 2       2399  831    3027 0.6040915 0.2660819    no voom_overallno          2
#> 4       2399  831    3027 0.6534296 0.3065134    no voom_overallno          2
#> 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
#>