COBRAPerformance object and constructor

The COBRAPerformance class holds various types of calculated performance measures. Objects from this class are typically generated from COBRAData objects by means of the function calculate_performance.

Usage

COBRAPerformance(
  fdrtpr = data.frame(),
  fdrtprcurve = data.frame(),
  fdrnbr = data.frame(),
  fdrnbrcurve = data.frame(),
  fsrnbr = data.frame(),
  fsrnbrcurve = data.frame(),
  tpr = data.frame(),
  fpr = data.frame(),
  splv = "",
  roc = data.frame(),
  fpc = data.frame(),
  deviation = data.frame(),
  onlyshared = NA,
  overlap = data.frame(),
  maxsplit = NA_integer_,
  corr = data.frame(),
  scatter = data.frame()
)

Arguments

fdrtpr

A data frame containing observed FDR and TPR values at various adjusted p-value thresholds.

fdrtprcurve

A data frame containing observed FDR and TPR values for a (potentially large) number of cutoffs applied to a 'score' (that can be p-value, adjusted p-value or a more general score).

fdrnbr

A data frame containing observed FDR and the number of features considered to be significant at various adjusted p-value thresholds.

fdrnbrcurve

A data frame containing observed FDR and number of features considered to be significant for a (potentially large) number of cutoffs applied to a 'score' (that can be p-value, adjusted p-value or a more general score).

fsrnbr

A data frame containing observed false sign rate (FSR) and the number of features considered to be significant at various s-value thresholds

fsrnbrcurve

A data frame containing observed false sign rate (FSR) and number of features considered to be significant for a (potentially large) number of cutoffs applied to the s-value

tpr

A data frame containing observed TPR values at various adjusted p-value thresholds.

fpr

A data frame containing observed FPR values at various adjusted p-value thresholds.

splv

A character string giving the name of the stratification factor, "none" if the results are not stratified.

roc

A data frame containing observed FPR and TPR values for a (potentially large) number of cutoffs applied to a 'score' (that can be p-value, adjusted p-value or a more general score), which can be used to generate a ROC curve.

fpc

A data frame containing observed numbers of false positive findings among the N top-ranked features (ranked by p-values, adjusted p-values or more general scores), for a (potentially large) number of Ns, which can be used to generate a false positive curve.

deviation

A data frame containing deviations between observed scores and true scores.

onlyshared

A logical value indicating whether only features shared between the results and the truth should be retained, or if all features present in the truth should be used.

overlap

A data frame or list of data frames with binary values indicating, for each of a number of methods and number of features, whether the method consider the feature 'positive' (significant, 1) or 'negative' (non-significant, 0). If it is a list of data frames, each list element corresponds to one level of a stratifying factor.

maxsplit

A numeric value indicating the largest number of levels to retain if the results have been stratified by an annotation.

corr

A data frame containing observed (Pearson and Spearman) correlation values between observed and true scores.

scatter

A data frame containing observed 'scores' (p-values, adjusted p-values or more general scores) and true scores, which can be used to generate scatter plots.

Value

A COBRAPerformance object.

Author

Charlotte Soneson

Examples

## Empty COBRAPerformance object
COBRAPerformance()
#> An object of class "COBRAPerformance"
#> @fdrtpr
#> data frame with 0 columns and 0 rows
#> 
#> @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] NA
#> 
#> @splv
#> [1] ""
#> 
#> @onlyshared
#> [1] NA
#>